Fishery is an essential part of economic and ecological civilization construction of Poyang Lake Ecological Economic Zone. Taking fishery development and ecological protection of Poyang Lake as research object, this paper elaborated the relation between fishery development and ecological protection from physiological characteristics and functions of fish species by the method of field survey and consulting related data. Finally, it came up with recommendations of increasing plagiognathops microlepis and Xenocypris davidi Bleeker and adopting and deepening healthy ecological and water body stratification. Besides, government organizations, local supervision authorities, scientific research institutions, and enterprise operating entities should jointly maintain and promote breakthrough mechanism for ecological balance of Poyang Lake water system.