Silicon (Si) can improve the resistance of rice to cadmium (Cd) effectively, but the response mechanisms of optimized Si fertilizer management on Cd tolerance, photosynthesis and matter accumulation of rice remain unclear. In this paper, pot experiments were conducted to study the effects of Si applied at transplanting stage (T), jointing stage (J), and split at transplanting and jointing stages (TJ) on photosynthetic characteristics and matter accumulation in rice. No Si application was used as the control (CK). The results showed that Si application effectively improved the net photosynthetic rate and extended the photosynthetic function of rice under Cd-pollution, promoted Si deposition in leaves, increased Cd immobilization in leaves, and reduced the transfer of Cd to grains. Compared with CK, the photosynthetic rate of TJ treatment was much higher in the whole growth period, and the yield of which was significantly higher than that of other treatments. The T, TJ, and J treatments increased the retention of Cd in leaf cell walls by 11.45%, 24.16%, and 30.15%, respectively, while more intracellular Cd existed in inert forms (including pectin and protein binding Cd, insoluble phosphoric acid Cd and residual Cd). Furthermore, the migration factors of Cd from leaves to grains were significantly decreased, and those of T, TJ and J were 33.91%, 56.67% and 52.16% lower than CK, respectively. In addition, principal component analysis showed that the comprehensive effect of the three Si treatments on Cd tolerance and photosynthetic characteristics of rice was expressed as TJ > J > T. Considering the effect of Si on photosynthesis, yield and Cd concentration in rice grains and leaves, it is recommended that Si application would be split at transplanting and jointing stage.