Purpose: There is little knowledge on the organic matter fractions of salt-affected soil aggregates. This study aimed at investigating characteristics of salt-affected soil organic carbon components and the relationships between soil salt concentration and soil organic carbon component content.Materials and methods: Five typical salt-affected soils in Hetao region China were collected and analyzed for light (LF) and heavy fraction (HF) in different water-stable aggregates. And the soil organic carbon components were measured by Fourier transform infrared (FTIR) and pyrolysis-gas chromatography/mass spectrometer (Py–GC/MS).Results and discussion: The results showed that the salt-affected soils were dominant in 53–10-μm water-stable aggregates, 61–80% in the bulk soil, and very low in > 250-μm macro-aggregates, less than 7.06% in the bulk soil. The proportions of > 250-μm macro-aggregates and the mean weight diameter (MWD) were negatively correlated to Na+ concentration (p < 0.05). Furthermore, the macro-aggregates were generally higher in total organic carbon (TOC) and accordingly higher C/N ratio than those in micro-aggregates. Heavy fractions (HF) from both > 53 μm and < 53-μm soil aggregates accounted for 99.30–99.83% of the bulk soil and contained 89.6–98.5% lower TOC and accordingly 49.2–84.8% lower C/N ratio than those in light fractions (LF). The LFs were high in lignin (7.27–34.02% in total pyrolysis products, 19.89% on average) and alkane/alkene-derived compounds (9.51–37.21%, 23.18% on average), but low in N-containing compounds (0–3.64%, 1.71% on average), while HFs were high in both alkane/alkene (4.38–27.46%, 15.06% on average) and N-containing compounds (7.45–26.45%, 13.98% on average), but low in lignin-derived compounds (1.13–8.75%, 3.86% on average).Conclusions: The tested salt-affected soils were predominant in 53–10-μm micro-aggregates, which was caused by the Na+ dispersion effect on soil aggregates. Most SOM was stored in HF that contained high N-containing compounds and low C/N ratios. Our results suggested that the components of SOM were mainly controlled by the soil Na+ concentration.