The evaluation of the in-situ gas content in deep coal seams, potentially containing free gas in saturated-oversaturated reservoirs, holds practical significance for exploration and production compared with shallow undersaturated-saturated reservoirs dominated by adsorbed gas. However, owing to the inherent limitations of volumetric and gravimetric methods, the accurate assessment of adsorbed and free gases faces significant challenges. In this study, based on molecular simulations, we focused on slit-shaped pores to explore the microscopic interaction mechanisms between coal and methane molecules under different pore sizes, temperatures, and pressures. By combining isothermal adsorption and pore structure experiments, the distribution characteristics of the adsorbed phase density (APD) and adsorbed phase volume (APV) were determined. The results showed that, in pores smaller than 1.5 nm, methane exhibited an aggregated state distribution (containing only adsorbed methane) characterized by micropore filling adsorption. In pores larger than 1.5 nm, methane showed a dispersed state distribution (coexistence of adsorbed and free methane) characterized by monolayer adsorption. The APD increased with pressure and decreased with temperature and pore size, whereas the APV remained independent of the pressure and temperature. In the in-situ gas content evaluation, three adsorption models (SL, SDR, and SL + SDR models) considering APV and APD were utilized to describe the methane adsorption behavior. The SDR model considering the APV was consistent with the actual physical properties and molecular simulation results. Traditional correction methods often lead to an overestimation of the adsorbed methane content, and neglecting the APV can result in an overestimation of the free methane content. In summary, the SDR model considering the APV can provide more rigorous scientific support for the refined study of methane occurrence states and gas content distribution.