To evaluate the river chief system in different levels and zones, we propose a matrix-based efficiency evaluation model that combines administrative grading with terrain and geomorphic zoning. Our evaluation index system for the river chief system is constructed based on seven aspects, including the six tasks of the river chief system and public involvement. We divide the index system into two levels: city and county level (18 indicators) and town and village level (16 indicators). We employ the Analytic Hierarchy Process (AHP) to determine the index weights for different characteristics of mountain and hilly areas, as well as plain and lakeside areas, and subsequently, we establish a two-level fuzzy comprehensive evaluation model to evaluate representative regions such as Ganzhou City, Nanchang City, Shangyou County, Zhangshu County, Meishui Town, and Zhangjiashan Street in Jiangxi Province. The evaluation results for these regions are categorized as good, medium, good, good, medium, and good, respectively. Our findings indicate that in hilly areas, the efficiency of the river chief system at all levels is mainly affected by water resource protection, whereas water ecological restoration influences the effectiveness of the system in Ganzhou City and Shangyou County. Additionally, water pollution control affects the effectiveness of the system in Shangyou County and Meishui Town. On the other hand, in plain and lakeside areas, water pollution control is identified as the primary factor impacting the efficiency of the river chief system at all levels. Water resource protection affects the effectiveness of the system in Nanchang City and Zhangshu County, while water ecological restoration also influences the effect in Zhangshu County. The evaluation results align well with the actual situation, affirming the suitability of our evaluation system for grading and zoning the efficiency of the river chief system.