Considering the negative impact of IUU fishing on fishery resources and fishery management, a revised approach for estimating risks of the ecosystem-based fisheries assessment (EBFA) of Zhang et al. (2011) was developed that incorporates three components of the IUU (illegal, unreported and unregulated) fishing as penalties. In this study, we introduced ways to develop indicators of IUU fishing suitable for the Korean fishery and apply them to ecosystem-based resource assessment. The indicator for the illegal fishing component was set as the fishing without licenses or permits, and that for the unreported fishing component was set as unreported fishing activities. Indicators for the unregulated fishing component were set as fishing operated by illegal fishing gear, illegal fish capture, fishing operations in prohibited fishing area, and fishing with restrict permits. IUU fishing significantly impacts the stock of target species. Therefore, in this study, the influence of IUU fishing is included in the Species Risk Index (SRI) at the species level, and weights are assigned based on the ratio of the stock, as     ․     . The revised ecosystem-based fisheries assessment method, which considers the impact of IUU fishing, was applied to major fisheries on the south coast of Korea. It is necessary to reduce the non-reporting rate through the expansion of the TAC system and improve the accuracy of statistical compilation. To this end, the electronic fishing reporting system, which is being implemented on all vessels in Korean distant water fishing vessels, should be introduced to the coastal and offshore fisheries as well.