The experiment was conducted to study the secondary metabolites of endophytic bacteria from onion by adopting purple and white onions as materials, endophytes were isolated by approaches of tissue separation, point sample of gradient dilution and streak plate, then they were screened and tested on the bacteriostatic activity by adopting indicators of 10 strains from face-to-face cultivation in PDA media. The fermentation liquor of antagonistic strain was detected using thin layer, chromatography(TLC) and high performance liquid chromatography (HPLC) by adopting onion extracts as control. A total number of 87 strains of endophytes were isolated from two onion species, including 68 strains of endophytic bacteria, 3 strains of endophytic actinomycetes, and 16 strains of endophytic fungi. Among of them, 12 strains had obvious antagonistic activity against 3 to 9 plant pathogens, accounting for 23.08% of the total, and 8 strains (YD–21, YD–23, YD–26, YD–27, YD–32, YD–38, YD–37, YD–22) had a broad antibacterial spectrum and antibacterial activity against 9 strains of indicator microbes. Results from the analysis of TLC and HPLC showed that liquor in YD–27 strain fermentation had Rf value of 0.73, similar to that of flavonoids extracts form onions. The strain of YD–27 could produce flavonoids or similar compounds, which showed that the endophytes had the potential ability to produce new drugs of flavonoids.