Studies of the effects of land-use change on soil physicochemical properties, microbial community structure and other biological properties are important for understanding changes in soil quality in agricultural soils. A diverse soil microbial community is an important measure of sustainable land use, and soil microbial community structure and diversity are sensitive indicators of soil quality. In recent years, land-use change from paddy field to economic forest land has been very common in the south of China. In order to recognize the effects of this land-use change on soil quality, a study was conducted, in Zhejiang province, on paddy and orchard surface soil (0-15 cm). Multivariate analyses including phospholipid Fatty Acids (PLFAs) were employed to determine the changes in soil environmental factors, microbial community structure and their relationships after land-use change from paddy fields to orchard farms. Water-stable aggregates (>0.25 mm), pH, organic matter (OM), base saturation (BS), total nitrogen (TN), Alkali-hydrolysable nitrogen (AHN) decreased after land-use change from paddy to orchard soils, and they had significant negative correlations with orchard age (P < 0.05). Enhancement of organic carbon mineralization and reductions in plant residues in the soil caused the decline in soil organic matter content which resulted in a reduction in water-stable aggregates (>0.25 mm) and total nitrogen. The increase in nitrification also led to a reduction in alkali hydrolyisable nitrogen. The extensive application of acidic fertilizer and enhancement of nitrification increased soil acidification (caused by H⁺). Microbial biomass carbon (MBC), microbial quotient (qMB) and soil respiration (Resp) decreased, and had significant negative correlations with orchard ages (P < 0.01). The changes in biological properties could be due to decreased soil moisture, OM and other soil characteristics. During the change from paddy field to orchard farm, soil microbial community structure changed: total phospholipid fatty acids (TPLFAs), PLFAs of bacteria, fungi, actinomycetes, protozoa, and specific microbial lipids decreased. Possibly because of enhancement of soil aeration, the ratio of protozoa to bacteria slightly increased. The ratios of Gram positive bacteria to Gram negative bacteria decreased significantly (P < 0.01). In contrast, aerobic bacteria to anaerobic bacteria and methanotrophic bacteria to total bacterial ratios increased significantly (P < 0.01). The ratios of fatty acids Iso to Anteiso and fatty acids cyclo to precurso increased significantly (P < 0.01), which implied that nutrient stress on soil microorganisms enhanced. Redundancy analysis (RDA) showed that the first 4 axes explained 95.6% of the cumulative variation of soil microbial community structure, which indicated that the 11 kinds of soil environmental factors were the main factors affecting the structure of the soil microbial community. Soil moisture, OM and AHN were the most important environmental factors to determine the differences in soil microbial community structure between paddy and orchard soils (P < 0.01). The analysis also indicated that land-use change had a greater effect on soil microbial community structure than orchard age. Our study concludes that after land-use change from paddy fields to orchard farms, soil physicochemical and biological properties degraded, and thus soil quality decreased. In contrast, a diverse soil microbial community was achieved and maintained in paddy soil systems, hence we predict that paddy fields are an effective way to maintain soil sustainability.