【Objective】 Trace elements are of vital importance in crop growth. Long-term application of micronutrient fertilizers may affect the distribution of the elements in farmland soil, therefore influencing crop yield and soil organic carbon composition. To explore the accumulations of trace elements in different size fractions of loess soil, we collected topsoils from field plots after 35 years of fertilization with Zn, Mn, and Cu. 【Method】 All the soil samples from the treated plots and control plots (CK) were fractionated into ≥250, 250-125, 125-63, 63-20, and ≤20 μm. The element contents, availability, and soil organic carbon content (SOC) were determined and compared. Also, the types and contents of organic functional groups in different size classes were determined using Fourier Transform Infrared (FTIR) spectrometer. 【Result】 The results show that the content of SOC in the treated plots was at a low level (6-12 g?kg-1) and was not significantly improved after applying Zn, Mn, and Cu fertilizers. Nevertheless, the three trace elements were enriched to different degrees: Zn and Cu fertilizers significantly increased the total contents of Zn and Cu (the degree of enrichment was above 10% and 100% respectively), but no evident Mn enrichment was observed under Mn fertilizer treatment (the degree of Mn was within 10%). The highest concentrations of Zn, Cu, and Mn were observed in the ≤20 μm fractions, but SOC stability in this fraction was the lowest, ranging between 0.30-0.32. This was mainly because of the greater content of the unstable functional group C-O, but lower contents of C=O, C=N, and C=C that were positively correlated with the recalcitrance of SOC. The functional groups (C-O, C=O, C=N) were positively associated with the accumulation of Cu in the soil. Also, the inconsistent relationships of Zn, Mn, and functional groups observed in the loess soil in this study suggest that the governing principals in this study were distinct from previous reports based on SOC-rich soils. 【Conclusion】Findings in this study suggest that long-term application of micronutrient fertilizers did not significantly change the content of organic carbon or organic carbon composition in the topsoil of our study area. Nevertheless, it enhanced the accumulation of Zn, Mn, and Cu in the micro-aggregates to varying degrees. This is affected by the total organic carbon, the content of organic functional groups, and the type and efficiency of elements adsorption together.