Thucydides is considered to be one of the great "fathers" of Western history, thus making his methodology the subject of much analysis in area of historiography.
Thucydides is one of the first western historians to employ a strict standard of chronology, recording events by year, with each year consisting of the summer campaign season and a less active winter season. This method contrasts sharply with Herodotus' earlier work The Histories, which jumps around chronologically and makes frequent and roundabout excursions into seemingly unrelated areas and time periods, and has set the standard for historiographical rigor to this day.
Thucydides also makes extensive use of speeches in order to elaborate on the event in question. While the inclusion of long first-person speeches is somewhat alien to modern historical method, in the context of ancient Greek oral culture speeches are expected. These include addresses given to troops by their generals before battles and numerous political speeches, both by Athenian and Spartan leaders, as well as debates between various parties. Of the speeches, the most famous is the funeral oration of Pericles, which is found in Book Two. Thucydides undoubtedly heard some of these speeches himself while for others he relied on eyewitness accounts.
These speeches are suspect in the eyes of Classicists, however, inasmuch as it is not sure to what degree Thucydides altered these speeches in order to most clearly elucidate the crux of the argument presented. Some of the speeches are probably fabricated according to his expectations of, as he puts it, "what was called for in each situation" (1.22.2).
Despite being an Athenian and a participant in the conflict, Thucydides is often regarded as having written a generally unbiased account of the conflict with respect to the sides involved in it. In the introduction to the piece he states, "my work is not a piece of writing designed to meet the taste of an immediate public, but was done to last for ever" (1.22.4).
There are scholars, however, who doubt this. Ernst Badian, for example has argued that Thucydides has a strong pro-Athenian bias. In keeping with this sort of doubt, other scholars claim that Thucydides had an ulterior motive in his Histories, specifically to create an epic comparable to those of the past such as the works of Homer, and that this led him to create a nonobjective dualism favoring the Athenians. The work does display a clear bias against certain people involved in the conflict, such as Cleon.
Role of religion
The gods play no active role in Thucydides' work. This is very different from Herodotus, who frequently mentions the role of the gods, as well as a nearly ubiquitous divine presence in the centuries-earlier poems of Homer. Instead, Thucydides regards history as being caused by the choices and actions of human beings.
Despite the absence of actions of the gods, religion and piety play critical roles in the actions of the Spartans, and to a lesser degree, the Athenians. Thus natural occurrences such as earthquake and eclipses were viewed as religiously significant (1.23.3; 7.50.4)
It has been further argued that Thucydides attributes the existence of the gods entirely to the needs of political life. The gods are portrayed as existing only in the minds of men. Religion as such reveals itself in the History to be not simply one type of social behavior among others, but what permeates the whole of social existence, permitting the emergence of justice.
Rationalization of myth
Despite the absence of the gods from Thucydides' work, he still draws heavily from the Greek mythos, especially from Homer, whose works are prominent in Greek mythology. Thucydides references Homer frequently as a source of information, but always adds a distancing clause, such as “Homer shows this, if that is sufficient evidence,” and “assuming we should trust Homer's poetry in this case too.” 
However, despite Thucydides' lack of trust in information that was not experienced firsthand, such as Homer's, he does use the poet's epics to infer facts about the Trojan War. For instance, while Thucydides considered the number of over 1,000 Greek ships sent to Troy to be a poetic exaggeration, he uses Homer's catalog of ships to determine the approximate number of Greek soldiers who were present. Later, Thucydides claims that since Homer never makes reference to a united Greek state, the pre-Hellenic nations must have been so disjointed that they could not organize properly to launch an effective campaign. In fact, Thucydides claims that Troy could have been conquered in half the time had the Greek leaders allocated resources properly and not sent a large portion of the army on raids for supplies.
Thucydides makes sure to inform his reader that he, unlike Homer, is not a poet prone to exaggeration, but instead a historian, whose stories may not give "momentary pleasure," but "whose intended meaning will be challenged by the truth of the facts."  By distancing himself from the storytelling practices of Homer, Thucydides makes it clear that while he does consider mythology and epics to be evidence, these works cannot be given much credibility, and that it takes an impartial and empirically minded historian, such as himself, to accurately portray the events of the past.