Film covers have been widely applied worldwide. However, the effects of long-term plastic film mulching use on heavy metal (HM) activity in soil remain unclear. This study focused on farmland in the upstream part of the Pearl River in China and collected 103 soil samples after 2, 5, and 15 years of plastic film mulching. The main environmental factors controlling microplastics (MPs), plasticizer phthalic acid esters (PAEs), HM pollution characteristics, and HM activity were analyzed. The results showed that Polyethylene (PE) and di(2-ethylhexyl) dicyclohexyl phthalate (DCHP) were the main MPs and PAEs, respectively. The abundance of MPs and the concentrations of free HM ions (Cd, Cu, and Ni) in the soil solution increased with increasing plastic film mulching duration. The Partial Least Squares Path Model (PLS-PM) indicated that after plastic film mulching, soil chemical properties (pH/amorphous Fe) and biological properties (Dissolved organic carbon/ Easily oxidizable carbon/Microbial biomass carbon) were the main controlling factors for free and complexed HM ions (Cd, Pb, Cu, and Ni). These results suggest that, after plastic film mulching, MPs indirectly regulate HM activity by altering soil properties. This study provides a new perspective for the management of MPs and HM activities in agricultural ecosystems.