Abstract: Objective Comprehensive evaluation of ecological clean small watershed construction in Gansu Province is essential for elucidating improvement mechanisms and constraints, thereby supporting the formulation of categorized governance and high-quality development paths. Methods Focusing on five typical ecological clean small watersheds in Gansu, this study established a composite evaluation index system. Comprehensive scores for 2023 (pre-construction) and 2025 (post-construction) were calculated to reveal the magnitude of effectiveness through dynamic comparison. Grey Relational Analysis, correlation analysis, and the obstacle degree model were employed to decipher driving mechanisms and limiting factors, followed by hierarchical clustering to categorize watersheds and design targeted governance strategies. Results 1) Construction effectiveness improved significantly, with the average comprehensive score increasing by 33.48% and regional disparities gradually narrowing. 2) NDVI, water quality, and village greening/beautification emerged as the primary driving factors. Conversely, forest and grass coverage exhibited a negative correlation with score improvement and the lowest relational grade, indicating a necessary strategic shift from scale expansion toward structural optimization and quality enhancement. 3) The average obstacle degree of indicators decreased by 39.01%. Critical bottlenecks shifted from non-point source pollution and infrastructure deficits to insufficient ecological-economic synergy, characterized by low agricultural commodity rates and short industrial chains. 4) Hierarchical clustering categorized the watersheds into three types: the Landscape Tourism Development type should refine environmental infrastructure and prioritize quality over scale; the Agricultural Economy Optimization type needs to promote green agriculture and specialty industries for synergy; and the Ecological Stability Transformation type should focus on enhancing ecological product value realization to bolster long-term internal drivers. Conclusions The dynamic evaluation method based on pre- and post-construction changes effectively identifies the driving mechanisms and phased characteristics of ecological clean small watershed construction. These findings provide a methodological and practical reference for implementing categorized governance and enhancing construction quality in Gansu and similar regions.