Polycyclic musks (PCMs) in soil environments have been of increasing concern because of their potential characteristic of persistence, bioaccumulation, and potential ecological risk. However, little is known about their fate process in soil environments. Here, we selected two PCMs as sorbates, namely galaxolide (HHCB) and tonalite (AHTN), to explore their sorption process in soils. Sorption batch experiments with six nature soils and their different aggregate fractions were carried out to elucidate the effect of organic–mineral interactions in different aggregate sizes on sorption of these two PCMs. The possible causes of variation in the organic carbon-normalized partition coefficient (Koc) for HHCB and AHTN have been investigated. The results indicated that the sorption contribution to different aggregate fractions to the overall sorption was dependent on both Koc and content of each aggregate fraction. The strong influence of organic–mineral interactions on Koc was evidenced by the large variation in Koc on HF-treatment for both bulk soils and their different aggregate fractions. This study verified the dual effect of organic–mineral interactions among selected soils. By comparing the measured and theoretical overlay ∆ Koc values, it was indicated that the interaction between particles of different size fractions will also affect Koc variation. This study represents a valuable contribution to the understanding of the fate processes and behaviors of PCMs in soil and its implication on the risk assessment.