Taking two medium-maturing indica rice hybrids Jinyou 63 and Shanyou 63 as test materials, this paper studied the effects of applying silicon fertilizer on the flag leaf chlorophyll content, photosynthetic properties, antioxidant enzyme activities, malondialdehyde (MDA) content, pollen vigor, anther acid invertase activity, pollination, and seed-setting of hybrid rice under the heat stress during anthesis. This study was conducted in pots and under growth chamber. Soluble solution of silicon fertilizer applied as Na2SiO3 x 9H2O was sprayed on the growing plants after early jointing stage, with three times successively and at an interval of one week. The pots were then moved into growth chamber to subject to normal temperature vs. high temperature (termed as heat stress) for five days. In treatment normal temperature, the average daily temperature was set at 26.6 degrees C, and the maximum daily temperature was set at 29.4 degres C; in treatment high temperature, the average and the maximum daily temperature were set at 33.2 degrees C and 40.1 degrees C, respectively. As compared with the control, applying silicon increased the flag leaf chlorophyll content significantly, improved the net photosynthetic rate and stomatal conductance, decreased the accumulative inter- cellular CO2 concentration, improved the leaf photosynthesis, reduced the MDA content, and improved the activities of SOD, POD and CAT under heat stress. In addition, applying silicon improved the anther acid invertase activity and the pollen vigor, increased the anther basal dehiscence width, total number of pollination per stigma, germinated number, germination rate of pollen, and percentage of florets with more than 10 germinated pollen grains, decreased the percentage of florets with fewer than 20 germinated pollen grains, and thus, alleviated the fertility loss of Jinyou 63 and Shanyou 63 under heat stress by 13.4% and 14.1%, respectively. It was suggested that spraying exogenous silicon in the early growth period of rice could mitigate the decrease of seed-setting at flowering stage, and improve the heat resistance of hybrid rice.