In purple soil region of southwest China, the eco-environment is extremely fragile in farmlands, and the application of green manure is facing serious problems. In order to improve soil health and explore the application way of green manure, the effects of intercropping green manure (Chinese milk vetch) on soil carbon, nitrogen and soil microbial in rapeseed rhizosphere was examined and compared with those of straw mulching. Chinese milk vetch was innovatively applied in dry land so as to establish a new rapeseed planting pattern in southwest China. Results showed that, compared with straw mulching, intercropping Chinese milk vetch was the main factor to affect soil environment in rapeseed rhizosphere. Intercropping Chinese milk vetch substantially decreased the content of carbon and total nitrogen and changed the C/N ratio in rapeseed rhizosphere. It also decreased the total PLFA (phospholipid fatty acid), changed the structure of soil microbial community, improved the soil aeration condition and inhibited the growth of anaerobic bacteria in rapeseed rhizosphere.