There is evidence of connections between soil organic carbon (SOC) and inorganic carbon (SIC) in dryland of north China. However, fractions of SOC and SIC and the relationship are not well understood in the Loess Plateau that undergoes profound erosion and redeposition. A study was conducted in low-elevation cropland of Loess Plateau across two distinctive basins: Lingfeng basin (LFB) with lower soil pH (< 8.4) and subject to erosion-redeposition, and Yuncheng basin (YCB) with higher soil pH (> 8.6) and under the influence of the Yellow River. Soil samples were collected from 30 sites over 100 cm. We determined SOC, SIC, dissolved organic carbon (DOC) and other properties. Above 100 cm, SOC stock is significantly higher in LFB (10.0 ± 2.6 kg C m− 2) than in YCB (6.9 ± 1.5 kg C m− 2), but SIC lower in LFB (14.0 ± 2.5 kg C m− 2) than in YCB (17.0 ± 5.7 kg C m− 2). We find a significantly negative correlation between SOC and SIC stocks in LFB, but no clear relationship in YCB. On average, DOC:SOC ratio is significantly higher below 40 cm in YCB (1.9%) than LFB (1.2%), indicating stronger DOC desorption in YCB that has stronger hydrological process due to the influence of the Yellow River. Overall, SOC has a negative correlation with SIC and soil pH, and DOC:SOC ratio has a significantly positive correlation with soil pH. Our analyses suggest that erosion/re-deposition of topsoil is partly responsible for the negative SIC-SOC relationship in LFB, and high soil pH and stronger hydrological processes are attributable to relatively lower levels of SOC in YCB. This study highlights that soil carbon fractions in the lowland of Loess Plateau are influenced by many drivers, which leads to complex relationships between major soil carbon pools.