Objectives The objective of this study was to analyze the characteristic change in soil organic carbon (SOC) density and the driving factors in China to provide a theoretical basis for soil fertility improvement, carbon sequestration, and food security.

Methods This study employs the national farmland monitoring database of the Ministry of Agriculture and Rural Affairs from 1988 to 2019 (1298 sites) to examine the spatial-temporal change in SOC density under paddy, upland, and upland-paddy rotations. Further, the effects of climate, fertilization, and soil properties on SOC density were investigated using equation fitting and boosting regression tree model.

Results From 1988 to 2019, the average SOC density in Chinese farmlands at the surface layer (0–20 cm) was 35.13 t/hm². The order of the SOC density was paddy soil > paddy-upland rotation soil > upland soil. The SOC density in paddy and paddy-upland rotation soil was 53.2% and 24.9% higher than in upland soil. The density of SOC decreased at first and subsequently increased as the monitoring time extended. The SOC density decreased before 2000, 1998, and 2004 in paddy, upland, and paddy-upland rotation, respectively, and subsequently increased. For paddy soil, SOC density increased in Northeast China (NE), decreased in South China (SC), decreased and then increased in Southwest China (SW, turning point was in 1995) and Middle of Yangzi River (MYR, turning point 2002) with the increase of monitoring time. The SOC density gradually increased in Northwest China (NW), North China (NC), and SC for upland soil. It decreased and then increased in NE (in 2008), MYR (in 2004), and Lower of Yangzi River (LYR, in 2004). For the paddy-upland rotation, the SOC density in MYR (in 2001) and LYR (in 2013) decreased at first and later increased with time while showing a slight and fluctuating trend of increase-decrease in SW (in 2012). The results of boosting regression tree showed that the most important explanatory variables in the rising stage of SOC density in paddy soils were mean annual temperature (MAT) in the SW, NE, and SC, potassium fertilizer input in the MYR, and soil available potassium in the LYR. For the raising stage of SOC density in upland soils, the most important explanatory variables were MAT in the NE, mean annual precipitation (MAP) in the NC and SC, nitrogen input (NF) in the MYR and LYR, and available phosphorus (AP) in the NW. For the paddy-upland rotation soils, the MAP, AP, and NF were the most important influencing factors of SOC density in the rising stage in the SW, MYR, and LYR regions, respectively.

Conclusions From 1988 to 2019, the density of surface SOC in paddy fields, dryland, and paddy-upland rotation field decreased before 2000, 1998, and 2004, respectively. Subsequently, there was a general increase in the SOC, except in the paddy field in South China. The main factors driving the change in SOC density were the annual temperature for the upland and paddy fields in the Northeast and Southwest China, potassium input and soil available K content for the paddy field, and nitrogen input for upland of Middle and Lower of Yangtze River. Moreover, annual temperature drives SOC in the paddy field and rainfall for the upland in South China; the rainfall and soil available P for the upland in North China and Northwest China; the soil available P for the paddy-upland rotation field in southwest China and Middle of Yangtze River; and soil available K for paddy-upland rotation field in Lower of Yangtze River.