Benzo[a]pyrene (B[a]P), a polycyclic aromatic hydrocarbons (PAHs) with the most carcinogenic effects, has multiple toxic effects on marine bivalves. In this study, we investigated the interference mechanism of B[a]P on the food metabolism (sugars, proteins and sugars), reproductive endocrine and ovarian development in female scallops (Chlamys farreri). Scallops were exposed to different concentrations of B[a]P concentrations of 0, 0.38, 3.8 and 38 μg/L throughout gonadal development. Total cholesterol (T‐CHO) and triglyceride (TG) contents in the digestive glands were increased and their synthesis genes were up‐regulated. The plasma glucose contents decreased with the inhibition of glycogen synthesis genes and the induction of glycolysis genes in the digestive gland. B[a]P showed endocrine disrupting effects on scallops, and negatively affected genes related to ovarian cell proliferation, sex differentiation and egg development and caused damage to ovarian tissue. The findings of this study supplement the information of B[a]P disruption in gonadal development of marine bivalves.