A unit stock is a basic assumption in fishery stock assessment. However, the stock always consists of local subpopulations or spawning subpopulations, among which there is some degree of exchange of individuals. Thus, the stock is commonly referred to as meta-population. We simulated two subpopulations of chub mackerel (Scomber japonicus) in the East China Sea and Yellow Sea based on the meta-population concept by setting up 12 scenarios. Using the data derived from the simulations and the surplus production model, we evaluated the effect of stock management based on 10 schemes, which involved different assumptions regarding the spatial structure of the stock and management strategies. The spatial structure of the stock was represented as 1) a meta-population, 2) two independent subpopulations or, 3) a unit stock. For management strategies, we focused on two methods of allocating the catch among the subpopulations: 1) assigning the catch in proportion to the biomass of each subpopulation or 2) assuming that the catch was uniform among the subpopulations by ignoring the spatial structure of the stock. Our results showed that (1) the maximum sustainable yield and the biomass at maximum sustainable yield could be achieved when there was little uncertainty in the CPUE and when the scheme was based on a meta-population assumption. However, the extinction probability of the stock increased with degradation of quality of the CPUE. (2) If we assumed there were two independent subpopulations by ignoring the exchange among the subpopulations, the stock was overfished and was not sustainable. (3) If the assessment and management was based on a unit stock assumption, the stock was either overfished or underexploited, depending on which CPUE was used as the abundance index of the stock, the methods of allocating catch along the subpopulations, and biological parameters such as the carrying capacity, intrinsic growth rate, and migration matrix. If the CPUE time series partially represented the trend of the biomass of the stock, for example by only representing the biomass of one of the subpopulations, there was a 100% probability of extinction under a certain situations. If the CPUE correctly reflected the dynamics of the biomass of the whole stock and the catch was assigned according to the biomass of each subpopulation, the effect of stock management was similar to (1), but it was suboptimal because the maximum sustainable yield could not be achieved. However, if the catch was allocated by ignoring the spatial structure of the stock, there was also a 100% probability of extinction under some situations. Therefore, to perform stock assessment and management for meta-populations, we recommend: (A) if enough information regarding subpopulations for stock assessment can be collected and there is little uncertainty in the observed data, the assessment and management of the stock should be based on a meta-population assumption. Otherwise, (B) a unit stock can be assumed but a more conservative management strategy should be adopted and a TAC (Total Allowed Catch) based on the spatial structure of the stock, i.e., the catch is allocated according to the abundance of the subpopulations, is needed to keep the fishery sustainable. (C) Before making a decision, the assessors or managers should conduct a management strategy evaluation to minimize management risk by evaluating the rules of management and taking into account the uncertainty in our understanding of the ecology of the species, collecting data, and assuming or estimating the parameters of the stock assessment model.