Abstract: OBJECTIVE To compare the contents of secondary metabolites and anti-bacterial activity of Ajuga decumbens Thunb and its two compounds, and provide a basis for reasonable compatibility of herbs. METHODS A oxford cup agar diffusion method was used to measure the anti-bacterial activity. The contents of secondary metabolites(flavonoids, saponins, iridoid and alkaloids) were determined by spectrometry. The correlation and path analysis were used to identify the goal compound. RESULTS The contents of flavonoids, saponins and iridoid were: compound 1>compound 2>Ajuga decumbens Thunb. The content of alkaloids was compound 2>Ajuga decumbens Thunb≈compound 1. The anti-bacterial activity of the two compounds was similar and significantly higher than Ajuga decumbens Thunb. The anti-bacterial activity of the 4 secondary metabolites was positive to staphylococcus aureus. The direct path coefficient of total iridoid was the highest of the secondary metabolites. CONCLUSION The contents of the secondary metabolites and anti-bacterial activity of the two compounds are higher than Ajuga decumbens Thunb. Iridoid and saponins are main components of antibacterial activity.