Bacterial wilt, caused by Ralstonia solanacearum (Rs) is a serious soil-borne disease, exogenous silicon application can enhance tomato resistance against this disease. The significant role of root exudates as belowground defense substances has well been documented. However, few studies have focused on the mechanisms of Si-mediated pathogen resistance from underground perspective. In this study, two tomato genotypes, HYT (susceptible) and H7996 (resistant), were used to investigate the impacts of silicon addition on disease inhibition, plant biomass, plant Si concentration, organic acid content in roots and root exudates under R. solanacearum infection. The result showed that Si treatment significantly suppressed bacterial wilt for HYT, but no effects for H7996. Silicon concentrations in roots, stems and leaves of tomato were significantly increased by Si treatment under R. solanacearum inoculation. Si application increased root dry weight and leaf photosynthesis by 22.8%-51.6% and 30.6%-208.0% for HYT, respectively. More interesting, the concentration of citric acid in root exudates and roots of HYT were significantly reduced by 71.4% and 83.5% in Si treated plant. Citric acid addition significantly stimulated R. solanacearum growth for HYT. Our results also demonstrated that salicylic acid (SA) content in roots was significantly increased by silicon after pathogen inoculation for H7996 and exogenous SA application could reduce bacterial wilt disease index. This study suggested that Si-modulated phenolic compound metabolism in roots or root exudates, especially citric acid and SA, may be a potential mechanism in the amelioration of bacterial wilt disease by Si.