The effects of two nitrogen (N) concentrations combining with three phosphorus (P) concentrations on Isochrysis zhangjiangensis growth and formation of fatty acid (FA) were investigated in this study. Biomass concentration, mass fraction, and productivity of FA in I. zhangjiangensis were low in N-deprived media. Under both N and P sufficiency conditions, the intake of P and N was 40 times and 4.7 times of the normal algal growth condition, respectively, indicating I. zhangjiangensis had the potential for removing P and N from high concentrated N and P salinity wastewater. This study also showed that P deficiency in N sufficient medium increased the FA content, however, the difference between P limitation and P deprivation was not significant (P>0.05). In N sufficient and P limitation medium, FA productivity was the highest, with a composition suitable for biofuel, so, this condition was the optimal condition for biodiesel production from I. zhangjiangensis.