To explore the effects of different nitrogen and phosphorus levels in water on the growth of diatoms, evaluate the indicative effect of diatoms on nutrient pollution, we chosed Navicula gregaria in this research. The response of main physiological indexes and cell morphological changes were determined and analyzed under different concentrations of nitrate nitrogen (NO^-₃N, 0.5-500 mg·L_-1), inorganic phosphorus (H₂PO^-₄P, 0.05-25 mg·L_-1) and N/P ratio (5∶1-100∶1). The results showed: (1) when the concentration of NO^-₃N, H₂PO^-₄P and the ratio of nitrogen and phosphorus were lower than 50 mg·L_-1, 1 mg·L_-1 and 50∶1, respectively, the cell density, chlorophyll a content and protein content increased gradually in the 13 days, while the MDA content, SOD and CAT enzyme activities in alga cells presented a continuous decrease trend. When the concentration of NO^-₃N was 50 mg·L_-1, the concentration of H₂PO^-₄P was 1 mg·L_-1, and the N/P ratio was 50∶1, the highest cell density, chlorophyll a content, protein content and specific growth rate were showed. Under high concentration of NO^-₃N (> 250 mg·L_-1), H₂PO^-₄P (> 5 mg·L_-1) and high N/P ratio (> 50∶1), cell density, chlorophyl a content and protein content of most of them decreased significantly, MDA content, SOD and CAT enzyme activities showed an obvious upward trend compared with other treatment groups. (2) It can be observed that at the 13th day, when the concentrations of NO^-₃N and H₂PO^-₄P are 500 mg·L_-1 and 25 mg·L_-1, respectively, the valve of Navicula gregaria showed obviously distortion, 8.6% and 7.2% of the cells were deformed, irregular surface, severe deformation of cells, widening of the central area of cells, micro tip of cell end and so on. The results indicated that the growth and physiological activity of algae could be promoted by properly increasing the concentration of nitrogen and phosphorus. However, when the ratio of nitrogen, phosphorus and nitrogen to phosphorus in the environment is high, the growth of algae will be affected, then eventually affect the structure of algae community structures in the water.