The influence of petroleum hydrocarbons (PHCs) on the transport and transformation of heavy metals may limit bioremediation efficiency. The mechanisms by which PHC degradation intermediates control heavy metal distribution in calcareous soils from karst areas require further exploration. This study systematically investigated how compositional changes in diesel fuel during aging regulated the fate of Cd and Pb in calcareous soils. The results demonstrated that the low-molecular-weight fractions of diesel fuel (C-C) were preferentially degraded. This degradation process altered zeta potential, cation exchange capacity (CEC), and pH, thereby promoting Cd stabilization through electrostatic attraction and speciation transformation. Particularly, reducible Cd content showed a strong positive correlation with C content ( = 0.88, < 0.05). Furthermore, the degradation of C-C fractions caused Pb transformation from residual to bioavailable fractions by stimulating microbial activity. Residual Pb content was positively correlated with C-C fractions ( = 0.55, < 0.05). Notably, dissolved organic matter (DOM) and CaCO content in calcareous soils enhanced Cd and Pb adsorption, thereby weakening the interactions between these metals and C-C fractions. Consequently, multiple linear regression (MLR) models relying exclusively on C-C degradation parameters showed poor fitting coefficients for Cd/Pb mobility. The present work provides scientific guidance for heavy metal bioremediation in calcareous soils.