Botrytis cinerea is a devastating phytopathogen causing great losses to many horticultural crops. As an important environment factor, light has a decisive influence on the formation of conidia and sclerotia of B. cinerea. Several light-responsive genes have been identified in B. cinerea, but the metabolic basis of photomorphogenesis is still unclear. In this study, we compared the metabolite profile of B. cinerea culturing under light and dark conditions by untargeted metabolomics. The results indicated that the metabolite composition of B. cinerea showed significant separation under different light conditions or at different developmental stages. The formation of sclerotia involves more metabolite rearrangement than the conidiation process of B. cinerea. The biomarkers of conidia and sclerotia of B. cinerea were screened based on ROC curve analysis. In addition, we screened out 6 metabolites strongly induced by light, among which ferulic acid had a significant effect on the photomorphogenesis of B. cinerea. The results of this study will help us better understand the light responsive mechanism of B. cinerea at metabolic level and lay a foundation for the control of fungal disease.