Soil organic carbon (SOC) is one of the most important soil attributes responsible for the sustainable maintenance of soil quality. In recent years, cropland withdrawal (CWD) (i.e., conversion into natural landscapes) in China has become a remarkable phenomenon of land use changes, driven by the spontaneous cropland abandonment by rural households and government‐led conversion of cropland to forest and grassland. The CWD may affect SOC content and storage in China. Therefore, this study estimated the variation in SOC caused by CWD between 1990 and 2018 based on the grid data of land use and soil organic matter (SOM). The results showed that CWD had a significant effect on SOC. (1) From 1990 to 2018, the total area of CWD was about 358 × 103 km2, an area that represented about 20% of the total area of cropland in China in 1990. In addition, within the total area of CWD, the proportions represented by the conversion of cropland to forest and grassland were the highest, reaching 58% and 39%, respectively. The former was mainly distributed in the southern part of China, especially in the southwestern mountainous area. The latter was largely concentrated in the northern part of China, especially in the Loess Plateau; (2) From 1990 to 2018, the average SOC content of CWD increased by about 10%, representing an increase of 193 Tg in soil organic carbon storage (SOCS). This is equivalent to six times the carbon emissions from agricultural land in China in 2019; (3) Among eight agricultural regions in China, the middle‐lower Yangtze Plain had the largest area of CWD, which accounted for 19.9% of the total CWD of the whole country.