The aroma profile of sweet oranges, a critical determinant of fruit quality, arises from complex interactions among volatile compounds rather than their simple summation. While existing studies focus on compound identification, the mechanistic basis of aroma interactions remains underexplored. This study innovatively integrates the S-curve method and molecular simulation to decode the molecular logic of aroma interplay in sweet oranges. This research identified 20 pairwise interactions among five key aroma compounds, revealing seven masking (1.2972 ≤ D ≤ 1.4333), 12 synergistic (0.1618 ≤ D ≤ 0.4958), and one additive effects (D = 0.6628). Notably, synergistic pairs exhibited structural complementarity, whereas masking pairs showed significant chemical divergence. Molecular dynamics (MD) simulations further showed that synergistic effects enhance system flexibility through induced-fit binding, while masking effects stabilize ligand-receptor complexes via competitive occupancy. Our findings establish computational modeling as a predictive tool for aroma optimization, offering novel strategies to engineer citrus flavors.