The heart has many metaphorical connotations, most of which are referred to at some point in the story. But arguably the most significant one of all is its symbolizing of the human soul. Most of the book's action, especially as it relates to Scobie, concerns the constant struggle with the voice of our conscience to do the right thing. The human heart—the soul—is fallible and weak despite our best efforts to keep on the straight and narrow.
The numerous moral dilemmas that Scobie encounters throughout the book are a prime example of this. For instance, Scobie was initially motivated by the very best of intentions in wanting to protect Helen, a malnourished survivor of a deadly shipwreck. But he soon embarks upon an illicit affair with her that entraps him in a web of sin from which he finds it harder and harder to escape. Indeed, the only way he can escape—through an act of suicide—is also a mortal sin for Catholics such as Scobie and so not even taking his own life can truly free his soul from its ceaseless torment. The heart of the matter is that Scobie's damned whatever he does.