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The properties of soil organic carbon (SOC) required for carbon sequestration and nutrient availability are contradictory, and the changes in SOC caused by agricultural land use changes remain elusive. Data on the total soil organic carbon (TOC) and labile organic carbon, including easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC), of the soil profile were analysed for four typical agricultural land use scenarios in the Chengdu Plain, China. The impacts of agricultural land use changes on sequestration and nutrient availability of SOC were assessed in this urban agricultural area using the space-for-time substitution method. Conversion of land use from a traditional agricultural rotation (rice-wheat/rapeseed rotation) to afforestation increased the MBC content and decreased the contents of EOC, DOC, and TOC due to the lower input of organic matter, improved aeration of the soil profile, and growth of aboveground biomass. Conversion of a traditional rotation to a rice-garlic rotation resulted in a significant increase in topsoil TOC, slight but insignificant decreases in subsoil TOC, and clear increases in labile organic carbon because of rice planting, rice straw mulch, and reasonable application of chemical fertilizers. In contrast, the conversion of a traditional rotation to a rice-leafy vegetable rotation decreased MBC due to the excessive use of chemical fertilizers that consequently increased EOC, DOC, and TOC. We conclude that afforestation on paddy soil has negative consequences for soil carbon sequestration and a rice-leafy vegetable rotation contributes to carbon sequestration but is detrimental to soil fertility. In addition, the MBC ratio in soil could be the optimal indicator for assessing SOC stability and soil fertility, and more attention should be paid to subsoil carbon changes.