Objectives In order to elucidate the antibacterial activity and mechanism of S. alboflavus TD-1 active metabolites, the minimal inhibitory concentration of R. solanacearum and other effects on cell wall, cell membrane, nucleic acid, protein and cell morphology were studied. Besides, based on LCMS-IT-TOF, the active metabolites of S. alboflavus TD-1 were preliminarily analyzed. Results In this study, We found that the active metabolites had obvious inhibitory effect on R. solanacearum, and the minimal inhibitory concentration (MIC) of R. solanacearum was 3.125 mg/mL. And the treatment of 10 mg/mL active metabolites can increase the permeability of R. solanacearum membranes, destroy the cell wall integrity, inhibit the synthesis of bacterial nucleic acids and proteins, and cause leakage of bacterial nucleic acids and proteins, obstruct the normal expression of proteins and destroy their bacterial morphology. At the same time, We speculated the molecular weights corresponding to the six compounds were 618, 615, 615, 615, 646, 646, respectively among the active metabolites, and it was found that were highly unstable. Conclusions The active metabolites produced by S. alboflavus TD-1 liquid fermentation contain components that can significant inhibitory effects on R. solanacearum. It had the potential to develop biocontrol agents against bacterial wilt and be a kind potential sources for the preparation of functional anti-pathogenic microbial agents.