The progressive replacement of conventional plastic films with biodegradable alternatives in agricultural systems has led to the accumulation of diverse plastic residues in soils, exerting documented impacts on microbial-mediated ecological processes. However, systematic investigations into how these residues influence organic carbon (C) turnover and inter-aggregate C flows remain critically lacking. This study investigated the effects of diverse plastic film residues on organic C decomposition dynamics and aggregate-associated C sequestration through a 60-day soil incubation experiment. Two representative plastic film types—conventional polyethylene (PE) and biodegradable polylactic acid + polybutylene adipate-co-terephthalate (PAT)—were incorporated into agricultural soil under contrasting organic matter input regimes: with maize straw addition (St) and without any straw addition. The results demonstrated that, in the absence of maize straw, both PE and PAT residues enhanced native soil organic C (SOC) mineralization. Notably, PAT elevated the cumulative CO2 emission by 7.4% (P < 0.05) relative to the control. PE slightly reduced the final SOC content but increased the proportion of soil gates (Mi) and silt plus clay (S + C) toward Ma. Conversely, PAT exerted a negligible effect on final SOC content but reduced Ma by 40.9% (P < 0.05) and increased Mi by 33.4% (P < 0.05), driving C redistribution from Ma to Mi. In contrast, with the addition of maize straw, both St + PE and St + PAT treatments reduced organic C mineralization and diminished the increases in SOC content. Specifically, St + PAT decreased the cumulative CO2 emission by 1.9% (P < 0.05) and lowered the SOC content by 7.1% (P < 0.05) compared to straw addition alone (St). Both St + PE and St + PAT also lowered Ma formation; notably, St + PAT significantly reduced Ma by 33.6% and diminished C flow from Mi and S + C into Ma. In conclusion, biodegradable film residues may impede SOC sequestration and macroaggregate-associated C storage by stimulating the mineralization of native SOC and suppressing organic matter decomposition after crop residue input in soil. These findings provide novel insights into the mechanisms governing SOC turnover and C stabilization via soil aggregation in the context of accumulating plastic wastes.