In order to elucidate the toxicity of NH4+ on Nostoc Sphaeroides (commonly named GE-XIAN-MI in China, GXM), a diazotrophic cyanobacterium in paddy fields, this study investigated the growth, photosynthesis, N2-fixation, and oxidative-antioxidative characteristics of GXM under NH4+ stress in paddy floodwater. The results showed that the photosynthesis and the N2-fixing ability of GXM were inhibited by NH4+ at a concentration of 13.46 mg L-1 in paddy floodwater. The main target of NH4+ on photosystem II (PS II) of GXM was the electron donor side of react center. Oxygen evolution complex (OEC) was the secondary target of toxicity of NH4+ on PS II. The damage of PS II led to accumulation of ROS and resulted in oxidative damage on plasma membrane of GXM. Feedback inhibition and decrease of photosynthetic energy production may be the reasons for the decrease of N2-fixing ability of GXM under NH4+ stress. The results presented in this study suggest that high level of NH4+ loading may be a reason for the recession of GXM resource in paddy fields.