Graham Greene saw The Heart of the Matter as dealing with the issue of pity. He illustrates this theme by describing Scobie, the main character of the book, as "a weak man with good intentions doomed by his big sense of pity". He further says in the preface, "I had meant the story of Scobie to enlarge a theme which I had touched on in The Ministry of Fear, the disastrous effect on human beings of pity as distinct from compassion. I had written in The Ministry of Fear: 'Pity is cruel. Pity destroys. Love isn't safe when pity's prowling around.' The character of Scobie was intended to show that pity can be the expression of an almost monstrous pride."
In the introduction, he says that the piece can be seen as a kind of exploration of his experiences in Sierra Leone as an operative for MI6 during World War II, drawing from his experiences almost directly for the work (such as the smuggled Portuguese letter found on a ship, which he did not allow to pass as in the book, but instead radioed up London asking "What was it all for?" to which he never received a response). In the preface of the novel he notes that the story originally came from a desire on his part to write a detective story where the principal character, the villain, is ignorant of who the detective is.
Whatever Greene's writings and personal feelings toward the story (he hated it and idly suggests that an earlier, failed piece whose place was given to The Heart of the Matter may well have been a better work), the themes of failure are threaded strongly throughout. Each character in the novel, be it Scobie or Wilson, fails in their ultimate goals by the end of the book. Scobie's ultimate sacrifice, suicide, fails to bring the expected happiness he imagines it will to his wife and despite the fact that he tries to conceal the secret of his infidelity with that ultimate sin, the reader discovers that his wife had known all along.
Similarly, Wilson, the man who is pursuing an adulterous affair with Scobie's wife, an affair she refuses to participate in, is foiled at the end of the novel when Scobie's wife refuses to give in to his advances even after Scobie's death. Other instances of failure, both subtler and more obvious, can be seen throughout the work, lending it a muted, dark feeling.
The Heart of the Matter is not just about failure, but about the price we all pay for our individualism and the impossibility of truly understanding another person. Each of the characters in the novel operates at tangential purposes which they often think are clear to others, or think are hidden from others, but are in fact not.
As in many of Greene's earlier works this book deals with not just the tension of the individual and the state, but also the conflict of the individual and the church. Scobie throughout the book constantly puts his fears in the voice and context of religion. After his wife returns he has a pathological fear of taking communion while suffering the stain of mortal sin and later agonises over the choice of suicide in terms of its theological damnation. The conflict is particularly interesting because it is not a conflict of faith, but rather a dispute set in legalistic terms: whether a violation of the laws of faith is justified by the personal sense of duty the character feels; which duty, personal or theological, is in the end primary; and what happens when those laws are broken. This argument is not simply one of whether Scobie is damned to hell, a question Greene himself tired of, but rather of whether what he did was worth anything in the world of the present.