In this study, the toxic effect of high ammonia on microalgae Tetraselmis cordiformis and the detoxification of phytohormones were researched. The growth, physiological changes, and gene transcription of T. cordiformis were examined. Malondialdehyde content was increased by 2.12 times compared with the control, suggesting the oxidative damage of T. cordiformis. However, the damaging effect of ammonia stress was significantly alleviated by exogenous phytohormones revealed by photosynthetic activity, antioxidant capacity, and nitrogen metabolism. Compared with cells exposed to 500 mg L-1 ammonia (NH4+-N), phytohormones increased the transcript abundance of photosynthesis-related gene (rbcL) by up to 10.95 times. Besides, after adding phytohormones, maximum activities of the antioxidant enzyme catalase (CAT) and nitrogen metabolism-related enzyme glutamine synthetase (GS) were 2.17 and 6.72 times that of the cells exposed to 500 mg L-1 NH4+-N. This study displayed the toxic mechanism of high ammonia on T. cordiformis, and also proved the detoxification of phytohormones.