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To reduce carbon emissions, hydrogen (H2) has been considered an important energy carrier, since its combustion only generates water. With the development of shale gas, depleted shale gas reservoirs might be good candidates for H2 storage. However, the mechanism of H2 storage in depleted shale gas reservoirs is not clearly understood. Therefore, in this work, we apply Monte Carlo simulation to analyze the compositional distribution and phase behavior of the H2–shale gas (H2–SG) system under multiscale (bulk + nanoscale) conditions. Our molecular simulation results show that compositional heterogeneity exists between the bulk region and the nanopores. The bulk fluid has a higher percentage of H2 while more hydrocarbons are present in nanopores. For the fluids in nanopores, hydrocarbons are adsorbed near the boundary while H2 molecules are freely distributed, which makes H2 molecules more likely to be released to the bulk region. The compositional heterogeneity and hydrocarbon adsorption collectively lead to a high percentage of H2 in the bulk fluid. Since the bulk fluid is produced during the extraction process, the high percentage of H2 in the bulk fluid means a high purity of H2 in the extracted fluid, which can be a positive factor for H2 storage in shale gas reservoirs. An increase in the volume percentage of nanopores can increase the H2 purity in the extracted fluid.