There has been increased scientific interest in the organic framing system which is one alternative to conventional agriculture. A long-term greenhouse soil of organic, low-input and conventional farming systems was studied, contrast analyses of the effects of organic farming system on soil nutrients, soil microbial biomass carbon and nitrogen and soil enzyme activities were made. The results showed after six-year experiments, the application of organic farming system could significantly increase soil total carbon and nitrogen content, and soil microbial biomass carbon and nitrogen content. The soil enzyme activities were improved. The performance indicators were organic system > low-input system > conventional system. The application of organic farming system could significantly improve soil quality and be conductive to the sustainable use of soil. The order of the yields of summer tomatoes was organic system > low-input system > conventional system. The autumn crop yields of organic system increased with planting years.