With aggravating water shortage in North China, rain-fed agriculture will become one of the trends of local food production. Therefore clarifying rain-fed agriculture effect on soil quality can provide a basis to estimate the change of crop yield. This study investigated soil enzyme activities and microbial functional diversities between long-term rain-fed farmland and traditional irrigated farmland and compared with nearby wasteland and woodland under four kinds of land use types of fluvor aquic soil in Fengqiu County, Henan Province. The dehydrogenase activity in rain-fed farmland decreased by 24% compared to irrigated farmland, however, the invertase, urease, alkaline phosphatase activities did not significantly differ from each other (P>0.05) and was higher than woodland and wasteland by 36%?–?149%. There were no significant differences in Biolog parameters including average well-color development and functional diversity indexes of soil microbial community. But the principal component analysis indicated that the ability of carbon source utilization in rain-fed farmland was close to irrigated farmland and woodland, but was greatly different from wasteland. The difference mainly attributed to different use of carboxylic acids and amino acids, which was probably related to higher pH in wasteland, as well as carboxylic acids and amino acids excreted from roots in rain-fed farmland, irrigated farmland and woodland. The results demonstrated that little change in soil enzyme activities and microbial functional diversity after 16 years’ rain-fed agriculture in fluvor aquic soil, indicating the feasibility of local rain-fed agriculture in the perspective of soil quality change.