Multispecies fisheries management requires managers to consider the impact of fishing activities on several species as fishing impacts both targeted and non-targeted species directly or indirectly in several ways. The intended goal of traditional fisheries management is to achieve maximum sustainable yield (MSY) from the targeted species, which on many occasions affect the targeted species as well as the entire ecosystem. Marine reserves are often acclaimed as the marine ecosystem management tool. Few attempts have been made to generalize the ecological effects of marine reserve on MSY policy. We examine here how MSY and population level in a prey-predator system are affected by the low, medium and high reserve size under different possible scenarios. Our simulation works shows that low reserve area, the value of MSY for prey exploitation is maximum when both prey and predator species have fast movement rate. For medium reserve size, our analysis revealed that the maximum value of MSY for prey exploitation is obtained when prey population has fast movement rate and predator population has slow movement rate. For high reserve area, the maximum value of MSY for prey’s exploitation is very low compared to the maximum value of MSY for prey’s exploitation in case of low and medium reserve. On the other hand, for low and medium reserve area, MSY for predator exploitation is maximum when both the species have fast movement rate.