On the surface, Heart of Darkness is an adventure story published in three parts. Because of this, each part ends on a cliffhanger designed to keep the reader interested. Objectively, it is hard to say if Joseph Conrad intentionally designed the structure of the story with any deeper meaning. However, it is possible to equate both the frame-story and the three-part structure to deeper meanings through specific context.
For example, the frame-story is a popular method of lending realism to a story. By presenting it as a story told by someone else, the narrator acts as a method of communication rather than of judgement, allowing the reader to examine the choices and morality of the story from a distance.
The three-part structure could, with some semantic context, be equated directly to the title. The first part is the "Heart," or the purpose behind the story itself. The second part is the "Of," which is not a noun, but could mean the Why and How of the journey itself. The third part is the "Darkness," or the ultimate goal and the discovery of the goal's meaning and purpose.
The structure could also represent Marlow's personal journey; he starts it literally in the present, on a ship, and then tells how he got there. The telling travels through the past and then, after explaining the consequences of Marlow's journey, returns to the present and ends, showing Marlow's personal change. Beginning and ending the story as a mature and cynical adult, and telling of his idealistic youth, Marlow explains exactly how he became the man he is today.