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Crop straw incorporation is widely recommended to maintain crop yields and improve soil organic carbon (SOC) stocks as well as soil quality. However, the long-term effects of different straw incorporation practices on the SOC stock remain uncertain. In this study, a long-term experiment (2007 to 2018) with four treatments (MW0: maize–wheat rotation with no straw incorporation, MW50: maize–wheat rotation with 50% chopped straw incorporation, MWb50: maize–wheat rotation with 50% burned straw incorporation, and MF50: maize–fallow rotation with 50% chopped straw incorporation) was setup to evaluate the response of the SOC stock to different straw incorporation methods. The results showed that the SOC stock significantly increased by 32.4, 12.2 and 17.4% under the MW50, MWb50and MF50treatments, respectively, after continuous straw incorporation for over a decade, while the SOC stock under MW0was significantly reduced by 22.9% after the 11 year long–term experiment. Compared to MW0, straw incorporation significantly increased organic carbon input, and improved the soil aggregate structure and the ratio of dissolved organic carbon (DOC) to particulate organic carbon (POC), but it did not significantly stimulate soil heterotrophic respiration, resulting in the increased SOC accumulation rate and SOC stocks of bulk soil. The increased ratio of DOC to microbial biomass carbon (MBC) enhanced the relative abundances of Acidobacteriaand Proteobacteriabut inhibited Bacteroidetesand Chloroflexi, and the bacterial relative abundances were the main reasons for the non-significant increase or even decrease in soil heterotrophic respiration with straw incorporation. The SOC stock would reach an equilibrium based on the results of Rothamsted Carbon (RothC) model simulations, with a long-term equilibrium value of 18.85 Mg ha-1under MW50. Overall, the results of the long-term field experiment (2007-2018) and RothC model simulation suggested that maize-wheat rotation with 50% chopped straw incorporation delivered the largest benefits for the SOC stock in calcareous soils of subtropical mountain landscapes over the long term.