Lipids produced from agricultural and industrial residues using oleaginous microorganisms for use as biofuels are attracting the attention of researchers due to their environmental benefits. However, low efficiencies and high costs limit their application to a certain extent. The present study is the first to use inositol as an enhancer to improve the production and accumulation of lipids during fermentation by the microalga Schizochytrium sp. SR21. The study aimed to maximize the production of lipids and docosahexaenoic acid (DHA) by optimizing the conditions of inositol addition into the fermentation medium. The corresponding key enzyme and metabolite profiles of SR21 were evaluated. The results indicated that the addition of 120mgL-1 of inositol to the medium at 48h improved lipid and DHA production by 13.90 and 20.82%, resulting in total concentrations of 22.86 and 8.53g/L, respectively. Moreover, the ratio of unsaturated fatty acids (UFAs) to saturated fatty acids (SFAs) increased by 23.38% and is consistent with the results of the metabolomic analysis. The activity of enzymes (i.e., PC, G6PDH, NADPH-ME, and ACL) related to fatty acid synthesis in strain SR21 also increased significantly (43.38%, 28.68%, 37.47%, and 19.87%, respectively). Metabolomic analysis also showed that inositol promoted lipid synthesis in SR21 and significantly increased the relative proportion of UFAs by affecting the citrate cycle and SFA and UFA metabolic pathways. Thus, inositol is an ideal enhancer of lipid production and accumulation by oleaginous microorganisms. Graphical abstract.