Background: Malate involves in the citrate/malate and transhydrogenase cycles to provide precursors for docosahexaenoic acid (DHA) synthesis. The optimal strategy was investigated for increasing DHA production in Schizochytrium species during fermentation. Results: DHA production increased by 47% and reached 5.51 g/L when 4 g malate/L was added during the rapid lipid accumulation stage in shake-flasks culture. Inducing effects of malate was further investigated through the analysis of three kinetic parameters, including specificcell growth rate(μ), specific glucose consumption rate (qGlu)and DHA formation rate (qDHA). DHA concentration was enhanced through a novel fed-batch strategy to a maximum value of 30.7 g/L, giving a yield of 0.103 g DHA/g glucose and a productivity of 284 mg L-1 h-1. Conclusion: A novel malate feeding strategy was developed that enhanced DHA yield and productivity of Schizochytrium species which may offer a desirable method for industrial applications