The film's central moral question (as in many of Burgess' books) is the definition of "goodness" and whether it makes sense to use aversion therapy to stop immoral behaviour. Stanley Kubrick, writing in Saturday Review, described the film as:
"...A social satire dealing with the question of whether behavioural psychology and psychological conditioning are dangerous new weapons for a totalitarian government to use to impose vast controls on its citizens and turn them into little more than robots."
Similarly, on the film production's call sheet (cited at greater length above), Kubrick wrote:
"It is a story of the dubious redemption of a teenage delinquent by condition-reflex therapy. It is, at the same time, a running lecture on free-will."
After aversion therapy, Alex behaves like a good member of society, but not by choice. His goodness is involuntary; he has become the titular clockwork orange — organic on the outside, mechanical on the inside. In the prison, after witnessing the Technique in action on Alex, the chaplain criticises it as false, arguing that true goodness must come from within. This leads to the theme of abusing liberties — personal, governmental, civil — by Alex, with two conflicting political forces, the Government and the Dissidents, both manipulating Alex for their purely political ends. The story critically portrays the "conservative" and "liberal" parties as equal, for using Alex as a means to their political ends: the writer Frank Alexander — a victim of Alex and gang — wants revenge against Alex and sees him as a means of definitively turning the populace against the incumbent government and its new regime. Mr. Alexander fears the new government; in telephonic conversation, he says:
"...Recruiting brutal young roughs into the police; proposing debilitating and will-sapping techniques of conditioning. Oh, we've seen it all before in other countries; the thin end of the wedge! Before we know where we are, we shall have the full apparatus of totalitarianism."
On the other side, the Minister of the Interior (the Government) jails Mr. Alexander (the Dissident Intellectual) on excuse of his endangering Alex (the People), rather than the government's totalitarian regime (described by Mr. Alexander). It is unclear whether or not he has been harmed; however, the Minister tells Alex that the writer has been denied the ability to write and produce "subversive" material that is critical of the incumbent government and meant to provoke political unrest.
It has been noted that Alex's immorality is reflected in the society in which he lives. The Cat Lady's love of hardcore pornographic art is comparable to Alex's taste for sex and violence. Lighter forms of pornographic content adorn Alex's parents' home and, in a later scene, Alex awakens in hospital from his coma, interrupting a nurse and doctor engaged in a sexual act.
Another critical target is the behaviourism or "behavioural psychology" propounded by psychologists John B. Watson and B. F. Skinner. Burgess disapproved of behaviourism, calling Skinner's book Beyond Freedom and Dignity (1971) "one of the most dangerous books ever written." Although behaviourism's limitations were conceded by its principal founder, Watson, Skinner argued that behaviour modification — specifically, operant conditioning (learned behaviours via systematic reward-and-punishment techniques) rather than the "classical" Watsonian conditioning — is the key to an ideal society. The film's Ludovico technique is widely perceived as a parody of aversion therapy which is a form of classical conditioning. Author Paul Duncan said of Alex: "Alex is the narrator so we see everything from his point of view, including his mental images. The implication is that all of the images, both real and imagined, are part of Alex's fantasies".  Psychiatrist Aaron Stern, the former head of the MPAA rating board, believed that Alex represents man in his natural state, the unconscious mind. Alex becomes "civilised" after receiving his Ludovico "cure", and the sickness in the aftermath Stern considered to be the "neurosis imposed by society". Kubrick stated to Philip Strick and Penelope Houston that he believed Alex "makes no attempt to deceive himself or the audience as to his total corruption or wickedness. He is the very personification of evil. On the other hand, he has winning qualities: his total candour, his wit, his intelligence and his energy; these are attractive qualities and ones, which I might add, which he shares with Richard III."