In this study, a conjoint analysis was conducted to derive a combination of fishing quota management system by fish species preferred by fishermen. In the analysis, detailed levels were set according to each attribute of the system. For analysis, this study conducted a design question survey for conjoint analysis on 303 fishermen engaged in fishing activities in the offshore and coastal sea. The Conjoint analysis was conducted on all fishermen, offshore fishermen and coastal fishermen. In addition, an analysis was conducted on TAC system participants and non-TAC system participants, and the targets were classified for comparison according to the characteristics of fishermen. Fishermen’s preference for the system confirmed for six attribute (“catching fish even if there is no fishing quota”, “how to allocate fishing quota”, “fishing quota management agency”, “upper limit of fishing quota,” “Possibility of Trading in the Fishing Quota”, and “Application of Other Regulations.”) and the detailed level of each attribute. As a result of the analysis of the importance of attributes, fishermen thought that “fishing quota management agency (24.1%)” was very important, and “catching fish even if there is no fishing quota (23.9%)” and “how to allocate fishing quotas (22.9%)” were also given some importance.