Kojic acid has significant anti‐melanogenic activity in mammals. However, few reports showed its function and mechanism in bivalves. In this study, by survival rate investigation and colour identification, 0.2–5 g/L kojic acid treatment for 24–48 hr was verified to be safe and effective to lighten shell colour of Pteria penguin (Röding; 1798). The liquid chromatograph–tandem mass spectrometer (LC‐MS/MS) analysis showed that the content of PDCA (pyrrole‐2, 3‐dicarboxylic acid) and PTCA (pyrrole‐2,3,5‐tricarboxylic acid), main alkaline oxidation products of eumelanin, were significantly decreased from 651.0 to 275.7 ng/mg (by 57.7%) after kojic acid treatment. Consistent with decrease in melanin content, the tyrosinase activity was also significantly inhibited by up to 54.7% in a dose‐dependent and time‐dependent manner. Different from the mammals, the qRT‐PCR (quantitative real‐time PCR) showed that kojic acid inhibited the expression of genes in tyrosinase pathway, including Tyr (Tyrosinase), Mitf (microphthalmia‐associated transcription factor), Yel (Yellow) and Cdk2 (cyclin‐dependent kinase 2), but had no effect on PpBcl2 (B‐cell lymphoma 2). These data indicated that kojic acid changed shell colour by blocking tyrosinase activity and negatively regulating transcription of tyrosinase pathway genes in P. penguin. The effectiveness of kojic acid in modifying nacre colour suggested potential for its application in the aquaculture production of higher quality cultured pearls in P. penguin.