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This study reports the effects of a long-term tillage and crop residue experiment on the soil microbial ecology of a Loess soil located in Gansu Province, western China. Tillage and residue management treatments were imposed on a nine-year continuous rotation of maize (Zea mays L. cv Zhongdan No. 2), winter wheat (Triticum aestivum L. cv Xifeng No. 24) and soybean (Glycine max L. cv Fengshou No. 12). After nine years, there were significant effects on topsoil (0-10 cm) carbon, nitrogen, microbial activity, microbial composition and function. The retention of crop residues compared to residue removal significantly improved all measures of chemical and biological soil fertility. The values of average well color development (AWCD), a measure of the metabolic utilization of organic compounds, for the residue retention treatments were always higher than those with residue removal treatments, and the differences increased with increasing incubation time. Principal component analysis indicated that crop residue retention significantly altered topsoil microbial activity and community functional diversity. Our research clearly demonstrates that retention of crop residues significantly enhances soil microbial metabolic capacity, compared to no tillage, and can therefore contribute to sustainable agriculture on the Loess Plateau. Promotion of conservation agriculture has the potential to rehabilitate soil fertility and improve agricultural sustainability and food security on the region.