Fucoxanthin (FX), a primary carotenoid, is associated with the fucoxanthin-chlorophyll a/c binding protein (FCP) complex integrated into the thylakoid membrane (TM) which functions as a light-harvesting complex in the diatom Phaeodactylum tricornutum. Here, we aimed to elucidate the FX production regulated by different light intensities via the correlation of FX biosynthesis and apoproteins composing of FCP complex. High light (HL) accelerated P. tricornutum growth more than low light (LL). The maximum values of FX content and productivity obtained under LL (1.7 mg g−1 and 2.12 mg L−1 day−1, respectively) were substantially higher than those obtained under HL (0.54 mg g−1 and 0.79 mg L−1 day−1, respectively). Notably, proteome and photosynthetic pigment analyses revealed the enrichment of FCP antennae in the LL culture TM fractions but not the HL culture. Semi-quantification of FCP antenna protein using LC–MS/MS and RNA transcriptome analyses revealed that PtLhcf5 and PtLhcf8 played crucial roles in FCP biosynthesis under LL. P. tricornutum cultured under light transition exhibited FCP formation only in the early growth stage to meet the increased photosynthetic activity requirements under LL. Meanwhile, FCP degradation could be triggered by HL throughout the cultivation period. Therefore, FX production was highly correlated with FCP formation, and LL conditions in the early growth stage were critical for higher FX productivity.