Four nutrient limitation cultures, namely monosodium glutamate (MSG-L), phosphate (P-L), ammonium sulfate (NH4+-L) and double (D-L, MSG and P limitation) limited, were designed to study how cell growth and biochemical components of Schizochytrium sp. were affected by nutrient limitations. All limited conditions caused decrease in biomass especially MSG-L and D-L conditions. MSG-L condition attained the highest lipid yield of 30.73 g/l but the lowest protein content. P-L condition shortened the fermentation time and obtained the highest DHA productivity of 291 mg/l h. D-L condition was the most cost-effective fermentation condition which gained the highest input-output ratio. NH4+-L condition got the highest squalene and DHA content in lipids. Meanwhile, nitrogen limited conditions promoted the accumulation of neutral lipids. All limited conditions benefit the PUFAs accumulation in the neutral lipids. In addition, the existence of NH4+ or the absence of MSG and phosphate reduced the unsaponifiable matters content in lipid. (c) 2014 Elsevier Ltd. All rights reserved.