China is in the transition period of eco-environment management. With the rapid economic development, aquatic ecosystems have been suffering a large number of ecological issues, such as water quality degradation, habitat loss, and biodiversity decline, which raised new requirements for the management, conservation, restoration, and regulation of aquatic ecosystems. However, the current aquatic environmental management is mainly based on water quality target management, which is not yet formed a conservation system that integrate multiple ecosystem elements (i.e., aquatic organisms, biological habitats, water quality and hydrology condition). On the basis of summarizing the relevant research results of aquatic ecology, this study sorted out and formed the conception and methodology of aquatic ecological conservation targets setting based on the theory of spatial and temporal scale, sensitive of biological organisms in response to multiple environmental stressors, and biological integrity of aquatic ecosystems. The response mechanisms of freshwater biological integrity to physical geographical elements, water quality and habitat condition were analyzed. We proposed a technical system of aquatic ecological target determination based on the principle of aquatic ecological function region zoning-aquatic ecological status assessment-eco-environment issues diagnosis-conservation target presetting-accessibility assessment-target determination. In addition, a series of key technical methods, such as development of evaluation index system, biological integrity assessment, aquatic ecological conservation targets presetting and accessibility analysis, were developed. Taking Changzhou as a case study, a typical application of an aquatic ecological functional region in Jiangsu Province, the applicability and feasibility of the technical system were verified. Aquatic organisms, water quality, habitat and hydrology conditions were monitored from 2017 to 2019. According to the evaluation method of aquatic ecological status, the individual indicators and different elements were assessed for each aquatic ecological function region, followed by a comprehensive evaluation of the aquatic ecological status. Further, the aquatic eco-environment issues in Changzhou were examined, the water ecological conservation targets were preset, the accessibility of the aquatic ecological conservation targets was evaluated and determined. The results showed that among the 17 aquatic ecological function regions in Changzhou, five regions failed to meet the preset targets, including 2 lake ecoregions and 3 river ecoregions. The aquatic ecological conservation target of the 5 ecoregions was reduced from "good" to "medium". It was finally determined that the aquatic ecological conservation targets were set as "good" in 4 ecoregions and the others set as "medium". The study was an examination of the theory and method of aquatic ecological conservation targets setting, which could provide references for eco-environment management in China.