The mid–Yunnan plateau is one of the major regions for the production of vegetables in China, but intense management practices have led to soil degradation and amplified greenhouse–gas emissions. Understanding management effects on soil organic carbon dynamics and structural stability can aid to improve vegetable cropping systems sustainability in this region. In the present study, we evaluated the effect of seasonal tillage alterations (non–winter–tillage [NWT] and winter–tillage [WT]) on soil (0–10cm) organic carbon (SOC) retention, soil aggregate stability, aggregate–associated C concentrations and CO2 emission in a clay loam soil. Results indicated after 2 years that the plots under NWT had nearly 4% higher total SOC content and 9% higher proportion of large macro-aggregates (>2mm) compared with WT plots in the 0–5cm layer. Greater SOC and labile C within large macro–aggregates in the plots under NWT compared with WT were also observed in the surface layer only. Soil CO2 emission rates were significantly greater in the WT plots than in the NWT plots during the dry season, but did not differ significantly between the WT and NWT plots during the rainy season. Our results demonstrated that the adoption of NWT should be a more sustainable management option than the traditional winter tillage for the maintenance of soil C and reduction of carbon dioxide emission in the rainfed vegetable cropping system of the mid–Yunnan plateau.