In the middle of the 1990s, Pacific saury fishery vessels began to install "size separators" to selectively land large-size class fish with a higher price. Contrary to expectations, this resulted in removal of the separators in 2006 because fishers believed the separators had contributed to price collapses in the 2000s. The intent of this paper is to investigate the effects of separators on both the fishery economy and stock of Pacific saury by simulating population and economic models under a single framework. For this purpose, we developed (1) an age-structured population dynamics model with stochasticity, and (2) an economic model spanning both price and inventory dynamics with stochasticity, in which each set of model parameters were estimated on the basis of time series data. In a 10-year simulation, the harvest quota was set constant from 20,000 to 400,000 t at intervals of 20,000 t, and the effects of separators were incorporated by controlling the catchability of 0-year-old fish. We found that separators increase the expected yield and reduce the deficit risk for harvests of 140,000 t and smaller. However, separators have the opposite effects for harvests of 160,000 t and larger.