In this study, the influences of major nutrients on cell growth and lipid production were investigated in heterotrophic culture of Chlorella protothecoides. The results demonstrated that phosphorus depletion had no effect on lipid accumulation but restricted cell growth; however, nitrogen depletion could enhance lipid accumulation thus benefiting lipid production. Furthermore, the effects of glucose inhibition were comparatively investigated with osmotic stress, showing that the effects of glucose inhibition were similar to the effect of osmotic stress at equivalent osmotic pressures only if the glucose concentration was less than 100 g/L, otherwise the effects of glucose inhibition became much stronger than osmotic stress. Interestingly, it was found that a specific hyperosmotic stress could significantly enhance lipid accumulation, thus providing a new stress strategy for efficient lipid production. Finally, a novel two-stage fed-batch culture consisting of a growth phase and a lipid accumulation phase with nitrogen depletion and hyperosmotic stress was proposed, yielding a final lipid productivity of 177.3 mg/L/h with a very high lipid yield of 207.0 mg/g glucose and lipid content of 39.2% after 180 h culture, which were 1.60, 1.79 and 1.92-fold of those obtained in one-stage fed-batch culture without stress phase, respectively.