Although natural gas hydrate is taken a potential energy resource, public concerns over environmental risks associated with hydrate exploitation are also growing, especially possible methane leakage to seafloor. However, whether hydrate exploitation can trigger disastrous methane blowout remains not well addressed. Overlying fine-grained sediments with poor seepage capacity are typically assumed to be good seals for methane. Yet, this view may be challenged when considering the geomechanical response of marine sediments, since sediment failure may provide new high-permeability pathways for methane flow. In this research, a new fracture module is supplemented into the Tough + Hydrate simulator to consider hydraulic fracturing of marine sediments. The modified simulator is employed to investigate methane behavior in the exploitation of hydrate reservoirs overlain by fine-grained sediments via the method of depressurization accompanied by warm water injection. Results suggest that overlying fine-grained sediments cannot necessarily seal methane during hydrate exploitation. The direct cause is that water injection elevates pore pressure above the critical stress of marine sediments and generates fractures. The fractured sediments provide pathways for the flow of mobile methane released from hydrate decomposition. Compared with control groups of simulations without the module executed, the results indicate that ignoring the fracturing process may cause significant underestimation of methane leakage when overlying fine-grained sediments exist. In addition, the results of simulations for the Shenhu area suggest that 0.3546–1.5432 Tg/yr may be leaked to the ocean with large-scale commercial hydrate exploitation in this area, contributing little to the global carbon budget.