The long-term stability of soil inorganic carbon (SIC) and its minimum contribution towards global C cycle has been challenged, as recent studies have showed rapid decreases in SIC stocks in intensive agricultural systems. However, the extent of SIC losses and its driving factors remains unclear. Here, we compared changes in SIC density (SICD) in Chinese croplands between the 1980s and 2010s. The SIC contents in 1980s were obtained from second national soil survey (n = 949) and published studies (n = 47). The SIC contents in 2010s were based on resampling of soil profiles from the same locations during 2019 and 2020 (n = 30), as well as data from published studies and national soil survey (n = 903). We found that Chinese croplands have lost 27–38% of SICD from the 0–40 cm soil layer and that the soil pH has decreased by 0.53 units over the past 30 years. These SIC losses increased with the ratio of precipitation (P) to potential evapotranspiration (PET) and most notably with nitrogen (N) fertilization. The SICD decreased greatly in humid and semiarid regions, and these losses were enhanced by high N fertilization rates; however, the SICD increased in very arid regions. This analysis demonstrates that the water balance and N fertilization are major drivers leading to dramatic losses of SICD in croplands and, consequently, to decreases in soil fertility and functions. © 2022