The heat-insensitive cultivar Chuangliangyou fengzhan, the intermediate cultivar Y liangyou 1 and the heat-sensitive cultivar Nongxiang 32 were used as experimental materials, and an artificial climate chamber was used for high temperature treatment at the heading stage(the maximum treatment temperature was 39.0 °C; relative humidity 75%-80%; light intensity 5.0×105 lx). The effects of high temperature stress at heading stage on pollen, anther and photosynthetic characteristics of rice were analyzed by measuring the characteristics, photosynthetic characteristics and appearance quality of pollen and anther under high temperature treatment and control treatment(field cultivation).The results showed that under high temperature stress, anther length of three rice varieties increased by 7.93%, 10.96% and 106.56%, and anther width increased by 30.99%, 56.79% and 106.54%, respectively. The anther volume increased by 84.62%, 167.92% and 764.00%, respectively. The pollen diameter increased by 5.83 μm, 3.50 μm and 2.60 μm , respectively. The fertile pollen rate decreased by 19.97%, 23.12% and 29.19%, stigma pollen number decreased by 10, 8 and 9, and stigma pollen germination rate decreased by 39.09%, 39.83% and 41.47%, respectively. The whole rice length of three varieties decreased by 4.59%, 5.66%, 13.12%,and width decreased by 2.01%, 3.18% , 10.42%, respectively. The length-width ratio decreased by 2.44%, 2.55% and 3.33%, respectively. The seed setting rate decreased by 23.39%, 24.59% and 49.49%, and the thousand grain weight decreased by 8.92%, 16.86% and 17.79%, respectively. Under high temperature stress, the chlorophyll fluorescence parameters of three rice varieties Fv/Fm decreased by 7.87%, 8.24%, 17.98%, ΦPSII decreased by 19.05%, 20.00%, 24.14%, qL decreased by 30.00%, 33.33%, 40.00%, respectively. YNO increased by 5.33%, 7.46% and 11.27%, respectively, indicating that its effective light energy utilization rate, photoreaction center activity and heat dissipation regulation ability decreased. With the stress relieved, Fv/Fm, ΦPSII, qL slowly increased, YNO slowly decreased, indicating that the effective light energy utilization rate, light reaction center activity and heat dissipation regulation ability slowly recovered. In conclusion, heat-insensitive cultivars had better pollen activity, scatter characteristics and photosynthetic characteristics than that of heat-sensitive cultivars, which may be the key factors of rice height tolerance.