Using microalgae as a feedstock for biofuel is a method to reduce carbon dioxide emissions. Nannochloropsis is among the most promising microalgal taxa for biofuel production. To improve the lipid productivity of the marine microalga Nannochloropsis sp. SCSIO-45217 a novel method involving phosphate (NaH 2 PO 4 ·2H 2 O) adjustment was established. First, the effects of phosphorous concentration on the lipid accumulation and biochemical composition of Nannochloropsis sp. SCSIO-45217 was studied in a batch culture. Subsequently, to enhance lipid productivity, a fed-batch cultivation mode was established with an initial phosphate concentration of 8 mg L −1 and continuous supplementation with 1, 2 and 3 mg L −1 phosphate, respectively, beginning on the 4 th day. In batch culture the lipid content increased gradually from 27.45 to 46.15% DW with decreasing phosphate concentrations. Along with the decrease in phosphate concentrations, the contents of neutral lipids, eicosapentaenoic acid (EPA) and polyunsaturated fatty acids (PUFAs) increased from 50.87 to 70.07%, 2.06 to 7.30% and 2.91 to 11.73% of the total lipid content, respectively. Lipid productivity was enhanced up to 127.20 mg L −1  day −1 in fed-batch culture, which was approximately threefold-fold higher than that of the low phosphate group (8 mg L −1 ). The productivity was 43.2% higher than that of the high phosphate group (40 mg L −1 ). These results indicated that Nannochloropsis sp. SCSIO-45217 can be a promising source for PUFAs and the optimized supply of phosphate in fed-batch cultivation is a suitable cultivation strategy for microalgal lipid production.