• Film mulching decreased soil organic C content in soil aggregates with 0.053–0.25 mm diameter.

• Fiber-shaped microplastics readily combined with the soil aggregates of 0.053–0.25 mm in diameter.

• Film- and granule-shaped microplastics were dominant in 0.25–2 mm soil aggregates.

• Natural and human activities changed the shape and size distribution of particle in soil.

Microplastic distribution is non-homogeneous in agricultural soil following plastic film degradation. However, the distribution of microplastics by shape and particle size in different soil aggregates remains unknown. To elucidate the distribution of microplastic shapes and particle sizes in soil aggregates with increasing years of film mulching, four paired fields with film mulching (FM) and no mulching (NM) were examined at 1, 5, 10, and 20 years after continuous mulching. An increase in soil aggregates of 0.053–0.25 mm diameter was observed; however, soil organic carbon content decreased after long-term FM. Microplastics primarily combined with 0.053–2 mm soil aggregates. Specifically, long-term FM was associated with dominance of film- and fiber-shaped microplastics in soil aggregates of 0.25–2 mm and 0.053–0.25 mm diameter, respectively. Fiber- and granule-shaped microplastics of 0.25–1 mm diameter primarily combined with 0.053–0.25 and 0.25–2 mm soil aggregates, respectively. Film-shaped microplastics of diameter > 1 mm and diameter 0.05–0.25 mm primarily combined with 0.25–2 mm soil aggregates. Therefore, distribution of microplastics in soil aggregates can be used to monitor soil health and quality, greatly enhancing our understanding of the risk posed by microplastics to the environment.