Purpose <p>Soil organic carbon (SOC) and its functional fractions are central to soil fertility and quality. However, the response of functional fractions to long-term nitrogen (N) and phosphorus (P) applications and their relative importance for C sequestration remain unclear.</p> Materials and methods <p>We designed an experiment on N and P applications in Inner Mongolia ‘s <i>Stipa baicalensis</i> meadow steppe. The experiment was set up with four treatments: control, N, P, and NP (100 kg N ha⁻¹ yr⁻¹ + 100 kg P ha⁻¹ yr⁻¹ ) to investigate the response of SOC and its functional fractions to long-term N and P applications.</p> Results and discussion <p>Compared with the control, the SOC content increased by 17.43%, 21.34%, and 41.17% respectively in the N, P, and NP treatments. Under the addition of N and P, fPOM (unprotected), Hdsilt + clay (chemical protection), and NHdsilt + clay (biochemical protection) increased by 153.76% ~ 261.29%, 10.00% ~ 60.65%, and 12.97% ~ 38.39% respectively. These fPOM, Hdsilt + clay, NHdsilt + clay fractions were positively correlated with potential organic C input (aboveground plant C + root C + root secretion C) and SOC. The N treatment primarily regulates the changes in the content of SOC and its functional fractions by increasing aboveground biomass (AGB) and decreasing pH. The P treatment primarily regulates the changes by increasing AGB and available P (AP). The NP treatment primarily regulates the changes by increasing AGB and AP, and decreasing pH.</p> Conclusions <p>Long-term addition of N and P in the meadow steppe leads to preferential stabilization of SOC in the fPOM fraction. Ultimately, this SOC is stably sequestered through the Hdsilt + clay and NHdsilt + clay fractions. This stabilization and transformation process is regulated by vegetation factors and soil factors, with the contribution of vegetation factors outweighing that of soil factors.</p> Graphical abstract <p></p>