This study identified problems of the existing ecosystem-based fisheries assessment approach, and suggested new methods for scoring risk and for the estimation of fishery risk index. First, risk scores of zero to two for target and limit reference points for each indicator were replaced by those of zero to three, and the risk scores were calculated from new formulae which were developed in this study. Second, a new method for estimating fishery risk index (FRI) was developed in this study, considering the level of indicators. New method was applied to the Korean large purse seine fishery, large pair trawl fishery and drag net fishery. More precise and detailed risk scores were obtained from the new method, which can explain the risks by the wider range of both risk levels for 'better than target' and 'beyond limit'. The new method for estimating FRI could avoid the basic problem related with duplicated computations of fishery-level indicators, which improved the estimated FRI to be more accurate. Also, a method for estimating variance of FRI using the bootstrap was proposed in this study.