<p>Water-based fracturing fluid is a commonly utilized agent in coal seam fracturing operations. However, its low flowback rate results in a considerable quantity of fracturing fluid remaining within the reservoir. The retention characteristics of different types of water-based fracturing fluids in deep coal-rock reservoirs, and the microscopic influence mechanism of these fluids on gas storage and desorption behavior, remain unclear. This work innovates a molecular model of a multi-nanopore composite representative of the matrix-cleat-slit system of a deep coal rock, and elucidates the retention characteristics of typical types of water-based fracturing fluids. A molecular simulation scenario, combining with molecular dynamics and grand canonical Monte Carlo, is designed to elucidate the microscopic mechanism of fracturing fluid retention affecting methane storage and desorption behavior. The findings indicate that the retention modes of fracturing fluid components in deep coal rock encompass cleat plugging, filter cake attachment, and filter cake plugging. The retention of fracturing fluid components reduces the storage capacity of methane by reducing the pore volume of the coal system and weakening the adsorption capacity of the coal wall. Fracturing fluid retention primarily exacerbates methane adsorption hysteresis through cleat plugging, and methane adsorption by the fracturing fluid network impedes methane desorption. The cleat plugging mode and the filter cake plugging mode impede the process of methane desorption within the coal matrix and cleat system, and the filter cake attachment mode inhibits methane desorption within the coal slit. The findings of this study can guide the selection and designation of water-based fracturing fluids, as well as the evaluation of production laws in deep coal-rock reservoirs.</p>