Although previous studies have indicated that Silicon nanoparticles (SiNPs) can reduce Cd uptake into rice, little information is available on the mechanism. Here, the hydroponically grown rice seedings exposed to Cd treatment in the presence or absence of Si NPs were characterized. The results showed that the presence of SiNPs alleviated Cd stress and restrained the translocation of Cd from roots to shoots. The morphological results showed that dramatic damage and severe structural changes in the root cells occurred in the absence of SiNPs, whereas the presence of SiNPs remained nearly intact cell structure of rice roots even in the presence of high concentrations of Cd. The subcellular distribution results showed that Cd content in cell wall of rice roots increased, and its concentration in cell organelle and soluble fractions decreased at SiNPs treatments, indicating that Cd was blocked in the cell wall by SiNPs. In addition, SiNPs alleviated the oxidative damage to rice roots, decreased the expression of genes involved in Cd uptake (OsNramp1 and OsNramp5) and activated the expression of genes involved in Cd transport into vacuoles (OsHMA3). This study provided a molecular-scale insight into the understanding of the SiNPs-reduced Cd uptake into rice.