Based on an systematic interpretation of the fundamental concepts, spatial distribution, and major classifications of non-perennial rivers, the dynamic characteristics of multiple elements such as water quantity, environmental conditions, and ecological features in non-perennial rivers are elucidated. The foundational theories for ecological management of non-perennial rivers, including ecological balance theory, community succession theory, and ecosystem regulation theory are explored. The basic principles for ecological environment governance of non-perennial rivers, namely problem orientation, tripartite collaboration, and integrated water resources management are proposed. A comprehensive “3+6+1” integrated framework is presented for ecological environment governance:“3” refers to the coordinated management of three spatial domains, including aquatic zones, riparian zones, and terrestrial areas; “6” represents six technical measures, including water allocation and conservation, pollution source control and interception, shoreline enhancement, endogenous pollution remediation, ecological network connectivity, and ecosystem restoration; “1”denotes the establishment of an intelligent management system. Building upon this framework, specific technical and management solutions for ecological environment governance of non-perennial rivers are proposed, while key priorities and development trends in this field are identified.