Knowledge about the changes in soil organic carbon (SOC) stocks and grain yields under different tillage and straw management is necessary to assess the feasibility and sustainability of conservation agriculture. An 8-year experiment was conducted in an intensive wheat (Triticum aestivum L.)–maize (Zea mays L.) rotation system in the southern Loess Plateau of China. Three tillage methods [control with no-tillage and straw removal (CK), no-tillage with straw stubbles 30–40 cm in height (NT), and rotary tillage with straw incorporation (RT)] were applied before maize planting, and two straw treatments [straw return (SR) and no straw return (SR0)] were applied after maize harvest. Thus, the treatments included CK-SR, CK-SR0, NT-SR, NT-SR0, RT-SR, and RT-SR0. Over 8 years, the SOC stock exhibited similar dynamic trends in all treatments, but was higher in NT, RT, and SR plots than in CK-SR0 plots. Compared with the initial soil, the SOC stock increased largest (34.1%) in NT-SR. Compared with the CK-SR0, the NT-SR, RT-SR, CK-SR, NT-SR0 and RT-SR0 increased the wheat grain yield by 47.2%, 36.8%, 24.9%, 25.1%, and 20.0%, respectively. The NT, RT and SR increased crop yield stability with the highest sustainable yield index in NT-SR for both wheat (0.67) and maize (0.70). This study showed the NT-SR was the best strategy for improving SOC stocks, grain yields and agricultural sustainability for the wheat-maize rotation system in northwestern China and other areas with similar climates and cropping systems.