This study explored the co-production of fucoxanthin and stearidonic acid from Isochrysis zhangjiangensis by investigating its carbon metabolism under different light intensities. Results showed high light inhibited the synthesis of fucoxanthin and stearidonic acid, while promoted cell growth and enhanced cellular lipid content compared with low light, achieving 2.4 g/L and 28.55%, respectively. Low light accelerated the accumulation of fucoxanthin and stearidonic acid, which obtained 23.29 mg/g and 17.16% (of total fatty acid). In combination with the molecular analysis, low light redirected carbon skeletons into glyceraldehyde-3-phosphate and diverted into carotenoid especially fucoxanthin. While, high light redistributed the skeletons to Malonyl CoA, citrate and alpha-Ketoglutarate and then oriented into lipid metabolism. The highest fucoxanthin and stearidonic acid productivity was 2.94 mg L-1 d(-1) and 4.33 mg L-1 d(-1), respectively, which revealed I. zhanjiangensis is a potential strain for the co-production of fucoxanthin and stearidonic acid.