Contamination of microplastics poses a serious threat to human life and has repercussions for other organisms’ natural systems. Microplastic pollution of the air, water, and soil is accelerating as a result of poor management and reckless handling of plastics in daily life. The occurrence and movement of microplastics in subterranean environments, particularly groundwater, have been extensively studied. Conversely, the presence of fractured rocks (on which many major cities have been raised) in the deep subsurface can affect the flow of pollutants and groundwater. The current models for aping pollutant transport in fractured porous media are designed for dissolved substances, making them unsuitable for studying microplastic behavior. This study aims to investigate the transport of microplastics through fractured porous media, considering the impact of skin formation. The transport of microplastics has been modeled by solving the set of non-linear partial differential equations using an implicit finite difference method. Preliminary findings indicate that fluid velocity plays a vital role in the migration of microplastic concentration along the flow direction. Furthermore, it is understood that when fractured skin is present, the diffusion of microplastics in the matrix is minimal. Several factors directly influencing the mobility of microplastics within the fracture-skin-matrix system include the linear partition coefficients, the effective diffusion coefficient of the fracture-skin, as well as the porosity of both the fracture-skin and fracture-matrix. As a result, in a heterogeneous fractured porous system, the presence of fracture skin inhibits the transport of microplastics.