Silicon (Si) is able to improve phosphorus (P) nutrition, but the underlying mechanism is still poorly understood. The aim of this study is to investigate the effects of silicon on phosphorus accumulation in different rice varieties including four indica and three japonica accessions in hydroponic solution. Addition of silicon significantly decreased shoot P concentration in both indica and japonica rice varieties, but hardly affected the root P concentration. Si did not affect P uptake, root-to-shoot translocation of P in all rice varieties, but improved P-use efficiency and increased ratios of P/Mn and P/Zn in plant. Gene expression analysis of P transporter (PT) genes showed that only OsPT6 was down-regulated by Si in japonica varieties, but not in indica varieties. The expression of other PT genes was unaffected by Si. Taken together, Si has different effects on P accumulation in different rice varieties and improved P-use efficiency is probably attributed to higher P/Mn and P/Zn ratios, resulting in higher P availability in plants.