Abstract: Some species of microalgae are considered as an ideal resource for biodiesel production because they contain high level of lipids. The traditional method to quantify the lipids level includes the solvent extraction and gravimetric determination based on a chloroform-methanol-water system. This method has the disadvantage of being time consuming and inefficient. Here we used Nile Red, a lipid-soluble fluorescent probe, to establish a novel method to determinate the level of lipids in microalgae rapidly and accurately. We applied the Nile Red method to investigate the dynamic accumulation of lipids in Isochrysis sp. CCMM5001 under different culture conditions. The results showed that there was a linear correlation between the lipids level and the cellular fluorescence of stained microalgal cells, therefore the former can be accurately indicated by the latter. Low nitrogen concentrations and low temperatures were suitable for accumulating of lipids. The level of lipids was reduced if the illumination intensity was overly high or low. On one hand the optimal conditions for the growth were: N concentration at 1323 mol/L, illumination intensity at 148.0 mol/(m2s), and the temperature at 25℃. On the other hand for the maximal accumulation of the lipids, the optimal values of the parameters above were 441 mol/L, 92.5 mol/(m2s), and 15℃ respectively. The culture condition was optimized and a two-stage cultivation was carried out to increase both the level and the production rate of lipids, the former reaching a high concentration of 63.3% and the latter reaching 22 mg/(Ld).