To effectively manage fishery resources, many studies suggest that the establishment of marine protection reserves (MPAs) lead to higher fishery yields than conventional management. The idea of MPAs is to allow fish stock to rebuild by creating a comprehensive protection for its habitat. It also yields benefits in terms of tourism and academic research. However, under the increasing uncertainty of marine environments, it is worthy to investigate whether MPAs still serve as a long-term optimal equilibrium of resource management and protection. The model in this study divides the marine environment into two areas: a fishing zone and a no-take zone, in which all fishing and extraction are prohibited. The latter preserves the original habitat, promotes the growth of fish stocks, and helps increase fishery yields in the fishing zone through spillover effect. Also, this study investigates the effects of environmental uncertainty on the profit maximization model and the open access model, along with the impacts of treating exploitation rate as an exogenous variable. Simulation results suggest that although fish stock will decrease with the increase of MPA sizes in the profit maximization model, the resources are still sustainable. Also, the increase of MPA sizes can stabilize the fishery yield in the long-run equilibrium even with uncertainty in the environment. In the open access model with exploitation rate treated as an exogenous variable, the results show that under all scenarios of uncertainty and exploitation rate, the fish stock rebuild better when the size of the protected area is at a high level in the long-run equilibrium.