This study is to clarify the changes of tomato plant growth and rhizosphere soil microbial functional community under different soil sources. The experiment was conducted with the disease-suppressive soil and tomato bacterial wilt disease, and the pot experiment and two fertilization modes were applied to investigate the effects of the disease-suppressive and -conductive soils on the rhizosphere microbial functional community structure and growth of pathogen Ralstonia solanacearum. The results show that: 1) The disease-suppressive soil has higher contents of organic carbon, available nitrogen, phosphorus and potassium, which enhance the growth of tomato and inhibit the occurrence of soil-borne diseases. The fresh weight of tomato shoots in SCOF (the disease-suppressive soil treated with organic-inorganic co-fertilization) is the highest (28.99 g/plant), increased significantly by 37.90% compared with the CCOF (the disease-conductive soil treated with organic-inorganic co-fertilization); 2) The soil treated with organic-inorganic co-fertilization inhibits the growth of pathogen Ralstonia solanacearum, and the growth of pathogen in SCOF and CCOF is decreased by 24.53% and 22.23% compared with the control respectively; 3) The soil treated with organic-inorganic co-fertilization and pathogen inoculation alters the rhizosphere microbial metabolic function. The rhizosphere microbial community in SCOF has stronger metabolic functional activity, and there are some changes in microbial populations that utilize carbon sources such as amino acids, carbohydrates, and polymers. Therefore, the disease-suppressive soil treated with organic-inorganic co-fertilization can help host plants to tolerant the stress of soil-borne diseases and maintain the healthy growth of host plants, which provides a perspective for the occurrence and control of soil borne diseases.