The sustainable use and benefit-sharing of aquatic genetic resources (AGRs) is a key component of the Convention on Biological Diversity, as well as an important topic in negotiation on an international legally binding instrument under the Convention on the Law of the Sea on the conservation and sustainable use of marine biological diversity of areas beyond national jurisdiction. However, the value of AGRs is difficult to define since its connotation has constantly under change along with technological development and new usage. This different opinions on its value has resulted in divergence in concept and difficulties in design of mechanism. In this context, this study aims to analyze the value composition of AGRs from the means to realize value of AGRs, and develop an approach for defining and evaluating the value of AGRs based on Total Economic Value (TEV) framework. Publicly accessible information was collected to find out the means to realize the value of AGRs. The result shows that the value can be realized in five means: commercial development, breeding, ecological use, management, and cultural value. Because the means to realize value of AGRs are not completely consistent with those of natural resources at the above-species level under the TEV framework, the TEV framework cannot be used satisfactorily to describe the value of AGRs, especially their derivatives and digital sequence information. As a result, the TEV framework is modified to fit the situation of AGRs’ utilization. The value of ARGs are composed of consumptive use value, non-consumable use value, selection value, existence value, and genetic value. Given the particularity of the value realization of AGRs, the modified TEV framework better matches the current usage of AGRs, and could effectively solve the divergency on the concept of AGRs in the negotiation and mechanism design. This study lays the foundation for value assessment of AGRs, promoting the establishment of a fair and reasonable benefit-sharing mechanism.