[Objective] This study aims to systematically analyze the evolution law of water environment under the overlapping impacts of non-point source pollution （NPSP） and rain-sewage pipe network misconnections，particularly within the unique context of mountainous cities. Given the steep terrain，complex drainage topologies，and fragile ecological conditions in the upper reaches of the Yangtze River，traditional management models developed for plain cities are inadequate in addressing the compound hydrological and pollution dynamics in this region. Therefore，the primary objective of this study is to quantify the specific pollution contributions of these overlapping factors and develop an adaptive，full-process collaborative control framework—covering source，pipe network，and terminal—that is tailored to the topographical and hydrological characteristics of mountainous cities，thereby providing a scientific paradigm for regional water environment management. [Methods] A typical mountainous city in the upper reaches of the Yangtze River was selected as the research case，and an integrated methodological approach was adopted. The empirical coefficient method was employed to systematically trace and quantify pollution loads from various sources，distinguishing between point-source and non-point source contributions. Subsequently，the Storm Water Management Model （SWMM） was established and calibrated to reflect the specific terrain-driven hydrological characteristics of the study area，such as rapid runoff convergence and steep pipe slopes. Based on these foundational analyses，multi-scenario simulations were designed and implemented，progressively comparing the effectiveness of isolated interventions with integrated strategies. This process ultimately led to the formulation and simulation of a collaborative control scheme integrating source （Low Impact Development，LID），pipe network （renovation），and terminal （storage tanks）. The SWMM model was then used to dynamically quantify the hydrological responses and pollution reduction effects under each scenario. [Results] The results provide critical insights into the pollution dynamics and control effectiveness in mountainous cities.（1） NPSP from urban runoff was identified as the dominant contributor to water environment degradation，with contribution rates of chemical oxygen demand （COD_Cr），ammonia nitrogen （${\mathit{NH}}_{4}^{+}$），and total phosphorus （TP） reaching 93.5%，74.6%，and 82.7%，respectively.（2） An assessment of the current drainage infrastructure revealed severe deficiencies： the existing annual runoff control rate was only 20%，and rain-sewage pipe network misconnections further exacerbated pollution，resulting in ammonia nitrogen concentrations at multiple overflow outlets that far exceeded the prescribed water quality standards.（3） Multi-scenario simulations demonstrated that isolated control measures are insufficient for mountainous terrains. In contrast，the implementation of the proposed coupled control scheme—integrating source LID facilities，pipe network renovation，and terminal storage tanks—achieved significant synergistic effects. This collaborative scheme increased the annual total runoff control rate from 20% to 60.5% and achieved a high annual NPSP reduction rate of 68.5% for total suspended solids （TSS）. Most notably，regarding the critical issue of overflow pollution，the compliance rate of ammonia nitrogen concentrations at overflow outlets reached an unprecedented 99.7%，effectively mitigating the severe contamination previously caused by rain-sewage mixing during storm events. [Conclusions] This study highlights the dominant role of NPSP and the critical vulnerability of misconnected rain-sewage pipe networks in shaping the water environment of mountainous cities. The core innovation of this research lies in the conceptualization and validation of a full-process “source-pipe network-terminal” collaborative control scheme specifically adapted to the terrain-driven characteristics of mountainous hydrology. Unlike conventional end-of-pipe treatments or isolated LID implementations，this integrated framework synergistically addresses the dual challenges of rapid runoff convergence and combined sewer overflows. The proven effectiveness of this coupled scheme—evidenced by substantial improvements in runoff control，TSS reduction，and near-complete ${\mathit{NH}}_{4}^{+}$ compliance—demonstrates that coordinated intervention throughout the entire drainage continuum is essential. Consequently，this full-process collaborative strategy effectively resolves the complex dilemma of NPSP control in mountainous cities，providing a transferable scientific paradigm and robust technical support for water environment governance in similar mountainous cities in the upper reaches of the Yangtze River and other regions.