In order to understand the distribution, occurrence forms, and influencing factors of chromium (Cr), nickel (Ni), and copper (Cu) in soil aggregates, a five-step extraction method was used to determine their forms in soil aggregates of different sizes in a mountainous area of northern Hebei Province. The ecological risk was evaluated using the geo-accumulation index (Igeo) and primary and secondary comparison value method (RSP). Redundancy analysis (RDA) was used to identify the main factors affecting the distribution and morphology of Cr, Ni, and Cu in soil. The results showed that in vertical distribution, Cr, Ni, and Cu were concentrated in the surface soil, but there was no clear relationship between soil depth and heavy metal content. The distribution characteristics revealed that Cr, Ni, and Cu in soils mainly existed in relatively stable Fe-Mn oxides and residue states, and their morphology in aggregates did not vary considerably with particle size. Furthermore, the RSP results showed that the pollution risk of Cr, Ni, and Cu was higher, with Cr and Ni posing the highest risk in the 0.5–1 mm and 1–2 mm particle size ranges. The RDA results showed that available phosphorus and soil organic matter (SOM) were the main factors that caused the characteristic difference of 1–2 mm aggregate components. Additionally, hydrolyzed nitrogen, cation exchange capacity (CEC), and calcium exchange have positive effects on the residual state of Cr. For Ni, SOM, CEC and exchangeable calcium have positive effects on the binding state of Fe and Mn oxides and carbonate. For Cu, CEC and exchangeable calcium are the key factors that cause the morphological differences of aggregates. Based on the above results, a theoretical basis has been provided for the prevention and control of pollution in the subsequent research area.