Deeper soil horizons might provide an opportunity to enhance C sequestration because soil organic matter (SOM) at depth is assumed to be stable. However, it is unknown whether the stable composition of organic carbon in subsoils changes with the length of cropping time and the type of soil. The objectives of this study were to determine the effects on the chemical structures of SOM of cropping time after conversion from grassland to arable land under a Phaeozem and Chernozem in northeast China. Near-quantitative multiple cross-polarization (multiCP) 13C nuclear magnetic resonance (NMR) spectroscopy was applied, and 11 types of carbon (C) functional groups were identified. Principal component analysis of these functional groups showed that the chemical composition of SOM was differentiated by soil type and depth. The Phaeozem and Chernozem profiles differed mainly in their relative proportions of aromatic C–C and (CH2)n groups: the Phaeozem contained relatively more aromatic C–C, whereas the Chernozem contained relatively more (CH2)n groups. The fused-ring aromatic C–C carbon was probably derived from char-like organic matter generated by burning of plant litter or from SOM humification, whereas the (CH2)n groups were likely to be from plant- or microbially-derived residues. The main differences between top- and sub-soils were the occurrence of more protonated C in the topsoils and more non-protonated C in the subsoils. With increasing length of cropping time, aromatic C–C and C–O groups and COO/N–C=O groups increased, but (CH2)n groups decreased in the Phaeozem subsoils and increased in the Chernozem subsoils. Our findings suggested that leaching and soil moisture might influence the origin, redistribution and transformation of the recalcitrant components of SOM in the soil profile, resulting in changes in SOM composition under different climates and soil types.