Hydroponic culture was conducted to study the effect of different nutritional conditions on the growth of Isoetes sinensis. The paper examined the changing rule of physiological and biochemical characteristics and photosynthetic fluorescence characteristics. The results showed that the chlorophyll content decreased but other physiological and biochemical indexes including soluble sugar content, malondialdehyde (MDA) content, proline (PRO) content, catalase (CAT) activity gradually increased as N and P concentrations increased in nutrient solution. And the peroxidase (POD) activity increased at the beginning then decreased. Among the photosynthetic fluorescence characteristics, the PSⅡ maximal quantum yield (F_v/F_m), PSⅡ effective quantum yield (Yield), photochemical quenching (qP), higher potential maximum relative electron transfer rates (P_m), initial slope of rapid light curve (α) and halfstarved value of light intensity (Ik) gradually decreased with N and P concentrations increased, while nonphotochemical quenching (qN) increased. We could conclude that Isoetes sinensis had a better tolerance to the stress of the medium nutrient condition but poor tolerance to the stress under the high nutrient condition with comparatively obvious physiological injury as N and P concentrations increased. The ability of osmotic adjustment and antioxidant capacity increased, but the photosynthesis capacity decreased with the high nutrient condition, The higher nitrogen and phosphorus could inhibit the physiological activities of Isoetes sinensis, and thus affected its growth. In terms of the possibility that one of the most important factors of endangerment of Isoetes sinensis attributes to the eutrophication water.