The invention provides a method for analyzing the molecular composition of mercaptan compounds in petroleum. The method comprises the following steps: dissolving a petroleum component into an organic solvent A, then adding a derivatization agent, carrying out reactions for 12 to 48 hours at a temperature of 0 to 80 DEG C; condensing the mixed solution after reactions, separating the solution by silica gel column chromatography, carrying out elution by using an organic solvent B, an organic solvent C, and an organic solvent D in sequence; condensing the mixed solution obtained in the elution step, individually dissolving the condensed solution into toluene and a mixed solvent of methanol, and then characterizing the molecular composition by adopting electrospray ionization-mass spectrometry. The provided analysis method can analyze the molecular composition of mercaptan in petroleum, especially heavy petroleum.