Abundances of reactive oxygen species produced by alga cells under the environmental stress can cause damages of alga cells, but cells are able to remove reactive oxygen by many means to protect cells for acclimation so as to build a potent recovery system including antioxidant enzyme such as superoxide Dismutase (SOD) and catalase (CAT). Effects of inorganic salts (N, P and salinity) on the antioxidant enzymes activities of Scrippsiella trochoidea were investigated in the present study. According to orthogonal experiment, antioxidant enzymes activities of Scrippsiella trochoidea cells cultured under different conditions were determined periodically. The results indicated that the variation of inorganic salts content has different degree effects on antioxidant enzymes activities. The varying of P content is the main contributor to the change of SOD and CAT activities, and the effects on SOD activities of N content is merely weaker than P. Salinity reveals no considerable effects on SOD and its effect on CAT activities is different at different phase.