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Seepage-type gas hydrate accumulation in subsea shallow formations involves complicated thermo-hydro-solid coupling processes and matching problem between various accumulation elements. The formation physical properties control local natural gas migration pathway and thus the final reservoir characteristics of hydrates. In this paper, a novel mixed-flux model for gas hydrate accumulation is established and then used to simulate the process of methane gas migration into the shallow stratum to form a hydrate reservoir. The effects of reservoir heterogeneity and gas source conditions on the distribution of pore fluid and hydrate accumulation are examined. The simulation results show that reservoir heterogeneity is conducive to the retention and lateral migration of CH4 in a hydrate stability zone. CH4 can contact more pore water to form a large hydrate reserve, but the formed hydrate is often dispersed. Low-permeability layers enhance the trapping of CH4 and form a uniform and large hydrate saturation. Besides, gas source conditions have an important impact on the hydrate accumulation in reservoirs. Large gas flux, small pore water flux, continuous gas supply, high content of heavy components in natural gas, and numerous gas source points contribute to large amounts of hydrates generation in a certain time period. The presented work will deepen our understanding of the controls of natural gas hydrate systems in subea shallow formations.