With intensifying global climate change and human activities, small-to-medium river ecosystems in the northern area of China are confronted with unparalleled thermal stress challenges. These rivers play a pivotal role in regional ecological balance, water resource provision, and biodiversity conservation. Although extant studies have addressed ecological restoration of rivers, most methodologies have predominantly focused on ecological responses under single-factor influences, overlooking the intricate coupling of multiple factors. Furthermore, exploration concerning the central role of biological activity and bio-regulation in thermal adaptability remains inadequate. This study aims to meticulously analyze the thermal equilibrium status of river ecosystems in northern China and proposes an optimized ecological restoration decision-making approach that considers multi-factor coupling. By assessing microbial activity indicators, conducting thermal equilibrium and bio-regulation analyses, and introducing a comprehensive decisionmaking framework, this research offers a scientific, systematic, and feasible strategy for the ecological restoration of small-to-medium rivers in northern China, serving also as a reference for parameter determination in wheat-corn Subsurface Drip Irrigation (SDI) in the North China Plain and for water-fertilizer management and decision-making.