Considering that the serious shortage of available silicon content in typical paddy soil of Hainan Island, it is urgent to make reasonable application of silicon fertilizer. In this study, paddy soils developed from five typical parent materials (basalt, marine sediments, fluvial alluvium, sand shale, and granite) in Hainan Island were selected to investigate the effect of silicon fertilizer application on rice in a field plot experiment. Rice yield, quality and the related physiological, biochemical and agronomic indicators under different silicon fertilizer treatments were analyzed. Results showed that compared with the blank control, the silicon fertilizer application in both T₂ and T₃ treatments significantly increased the rice yield and its related indicators such as the number of stem tillers and effective heads, seed rates, 1000-grain weight, root activity, chlorophyll and crude cellulose content relative to the control. Rice quality such as milled rice, chalkiness and amylose content also reached a good level. It is generally recommended that the optimal amounts of Si fertilizer application are 750-950 kg/hm² (available SiO₂: 187-238 kg/hm²) for basalt-developed paddy soil and 625-935 kg/hm² (available SiO₂: 156-234 kg/hm²) for granite-developed paddy soil, respectively. Meanwhile, compared with the control, the amount of silicon fertilizer application in T₂ and T₃ treatments significantly increased the number of tillers, root activity, chlorophyll and crude cellulose content in paddy soil developed from marine sediments, river alluvial and sand shale. Rice yield reached the highest and rice quality reached a good level in T₂ treatment, but rice yield and its related agronomic indicators did not increase significantly with the increasing of silicon fertilizer application (T₃), and even some indicators exhibited a downward trend. It is recommended that the optimal amounts of Si fertilizer application are 560 kg/hm² (140 kg/hm² of available SiO₂) for paddy soil developed from marine sediments and river alluvial sediments, and 750 kg/hm² of silicon fertilizer (187 kg/hm² of available SiO₂) for paddy soil developed from sandy shale, respectively. Thus, this study revealed the effect of silicon fertilizer application in typical paddy soil of Hainan Island, providing a scientific basis for formulating the standard of silicon fertilizer application as well as demonstrating and popularizing high efficiency silicon application technology and of rice in Hainan province.