Mountainous rivers are mainly characterized by many shoals, rapids and curved channels. Based on the waterway regulation projects of Luzhou to Chongqing and Yibin to Luzhou reaches located in the upper reach of Yangtze River, this paper analyzes some main factors of systemic treatment and comprehensive treatment approaches for long reach and puts forward design methods of systematic treatment for the long reach, which can provide reference for the systematic treatment on mountainous rivers.