Tobacco soil-borne diseases have caused severe damage to tobacco production in Guizhou Province. The investigation of the effect of different varieties of green manure on suppressing the bacterial wilt pathogen (Ralstonia solanacearum, Rs) and improving soil microbial activity will provide new ideas and methods for bio-controlling soil-borne diseases. In this research, 15 green manure varieties suitable for planting in southwest tobacco areas were selected. Pot experiments and field trials were conducted to prove the inhibition effect of green manures on Rs and the black shank pathogen (Phytophthora parasitica var. nicotianae, Pn) in the soil. Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) technology was employed to identify and quantify the main substances in root exudates of green manures. Fluorescence quantitative polymerase chain reaction (PCR) was used to study the effect of root exudates on the population of Rs and Pn. High-throughput sequencing of soil microbes was applied to reveal soil microbial community structure and functional gene metabolic expression. (1) The population of Rs in the mung bean planted soil was only 31.26 % of that in the control treatment 80 days after planting, while the number of Pn in February orchid planted soil was only 36.16 % of that in the control treatment. (2) The inhibitory effect of mung bean root exudate on Rs was strongest, with an inhibitory rate of 69.05 %. The root exudates of February orchid had the most obvious inhibitory effect on Pn, with an inhibitory rate of 88.3 %. (3) The root exudates of four green manures were mainly organic acids, amino acids and carbohydrates. The content of amino acids and organic acids in the root exudates of February orchid was higher than any other green manures. The organic acid in the root exudates of February orchid contained 0.72 mg/kg of lactic acid, which was not detected in that of other green manures. The palmitic acid content of legume green manure, including mung bean and hairy vetch was 48.58 % higher on average than that of cruciferous green manure, including rape and February orchid. Besides, only arabinose was detected in the carbohydrates in the root exudates of green manure, with an average content of 2.32 mg/L. (4) After applying green manure in the field, the highest control efficacies of bacterial wilt and black shank were mung bean (55.61 %), and hairy vetch (68.69 %), respectively. (5) The abundance of Rs in the control rhizosphere soil was significantly higher than that in green manure-planted soil, which were 4.35, 4.14, 2.90 and 2.29 times of rape, hairy vetch, mung bean and February orchid, respectively. The abundance of a-Proteobacteria (Alphaproteobacteria), Myxobacteria (Haliangium) and Klebsiella were higher in mung bean treatment than other treatments; Phytophthora was not detected in any treatments, while the abundance of fungi such as Fusarium and Chaetomium was highest in the control among all the green manure treatments. (6) The soil functions, such as amino acid metabolism, transcription, replication and repair, were enhanced after treatment with green manures. In summary, root exudates of green manure greatly affect the population of soil-borne pathogens. After the application of green manure, the structure and function of soil microbial communities were changed. Mung beans and February orchids are suitable for biological control of bacterial wilt and black shank. The research results provide a new way for greener prevention and control.