Flooding is an important natural disaster limiting rice production. Silicon (Si) has been shown to have an important role in alleviating varied environmental stress. However, very few studies have investigated the effects and mechanisms of Si in alleviating flood stress in rice. In the present study, wild type rice (cv. Oochikara, WT) and Si-defective mutant (lsi1) were chosen to examine the impacts of Si application on plant growth, photosynthesis, cell structure, and antioxidant enzyme activity of rice exposed to submergence stress at tillering stage. Our results showed that Si application improved root morphological traits, and increased Si uptake and plant biomass of WT under submergence stress, but non-significantly influenced lsi1 mutant. Under submergence stress, leaf photosynthesis of WT was significantly inhibited, and Si application had no significant effects on photosynthetic rate, transpiration rate, stomatal conductance, and intercellular carbon dioxide concentration for both of WT and lsi1 mutant, but the photochemical quenching of WT was increased and the integrity of cell structure was improved. In addition, Si application significantly reduced malondialdehyde concentration and increased the activity of peroxidase and catalase in WT leaves under submergence stress. These results suggested that Si could increase rice plant resistance against submergence stress by improving root morphological traits and chloroplast ultrastructure and enhancing antioxidant defense.