The influence of reactive nitrogen (N) and phosphorus (P) supplementation on ecosystem dynamics of soil organic matter (SOM) shows extensive variations. The underlying mechanisms of regulation of the chemical composition and dynamics of different SOM density fractions (DFs) in aggregates in a desert steppe by N and P supplementation are unclear. Here, the chemical composition and organic carbon (C) and N dynamics of various SOM DFs under N and P addition were assessed. Surface soil samples taken at 0–10 cm depth were obtained from 4-year (2017–2021) experiments under four conditions, namely N treatment, P treatment, combined N and P treatment (NP), and no nutrient supplementation (CK), in a desert steppe located in northern China. Nutrient supplementation significantly increased (P < 0.05) SOM content by 8.89–35.4%; however, the total N content remained constant. N addition mainly increased SOM content in the macroaggregates (>0.25 mm), while P enhanced SOM in microaggregates (0.25–0.053 mm) and silt-clay (<0.053 mm). The fine particulate organic matter (fPOM) proportion was increased significantly (P < 0.05) by 18.4% and 16.4% in macro- and microaggregates under N addition, respectively; P addition mainly enhanced mineral-associated SOM (mSOM) proportion in aggregates. N supplementation remarkably enhanced (P < 0.05) fPOM’s organic C content by 27.3% and 32.0%, and N content by 40.9% and 145.7% in macro- and microaggregates, respectively. Single N and P addition promoted the enrichment of labile and resistant organic components in light fraction (LF), respectively. N promoted the enrichment of stable organic components in the mSOM of microaggregates. Nutrient inputs drive mSOM formation through the interaction of carboxyl-C and mineral surface. Based on a stronger δ13C and δ15N signal, N addition enhanced SOM decomposition in aggregates. Nutrient supplementation promoted SOM accumulation through the formation of more stable old C in POM and silt-clay. Our findings suggest that SOM accumulation in desert steppe probably increases following nutrient addition, but the mechanism is different through which N or P enrichment affects soil dynamics and chemical composition of SOM DFs in desert steppe.