While the book pokes fun at contemporary society, the main thrust is a satire of romanticized ideas of chivalry, and of the idealization of the Middle Ages common in the novels of Sir Walter Scott and other 19th century literature. Twain had a particular dislike for Scott, blaming his kind of romanticism of battle for the southern states deciding to fight the American Civil War. He writes in Life on the Mississippi:
It was Sir Walter that made every gentleman in the South a Major or a Colonel, or a General or a Judge, before the war; and it was he, also, that made these gentlemen value these bogus decorations. For it was he that created rank and caste down there, and also reverence for rank and caste, and pride and pleasure in them. [...] Sir Walter had so large a hand in making Southern character, as it existed before the war, that he is in great measure responsible for the war.—Mark Twain, Life on the Mississippi.
For example, the book portrays the medieval people as being very gullible, as when Merlin makes a "veil of invisibility", which according to him will make the wearer imperceptible to his enemies, though friends can still see him. The knight Sir Sagramor wears it to fight Hank, who pretends he cannot see Sagramor for effect to the audience.
Hank Morgan's opinions are also strongly denunciatory towards the Catholic Church of the medieval period; the Church is seen by the Yankee as an oppressive institution that stifles science and teaches meekness to peasants only as a means of preventing the overthrow of Church rule and taxation. The book also contains many depictions and condemnations of the dangers of superstition and the horrors of medieval slavery.
It is possible to see the book as an important transitional work for Twain, in that earlier, sunnier passages recall the frontier humor of his tall tales like The Celebrated Jumping Frog of Calaveras County, while the corrosive view of human behavior in the apocalyptic latter chapters is more akin to darker, later Twain works like The Mysterious Stranger and Letters from the Earth.
George Hardy notes that "(...) The final scenes of 'Connecticut Yankee' depict a mass force attempting to storm a position defended by wire and machine guns - and getting massacred, none reaching their objective. Deduct the fantasy anachronism of the assailants being Medieval knights, and you get a chillingly accurate prediction of a typical First World War battle. (...) The modern soldiers of 1914 with their bayonets had no more chance to win such a fight than Twain's knights"