The river chief system is an institutional innovation for river and lake management and protection based on regional management. Insufficient watershed management and a lack of trans-provincial cooperation are the weaknesses in fully implementing the river chief system. Through discussion and communication, data collection and field research, we sort out the progresses of implementing river chief system in Dongjiang River, a typical trans-provincial river in the Pearl River Basin, and systematically summarize the experiences and lessons learned from the joint protection and management practices. We also put forward some suggestions as follows: promoting river basin coordination, accelerating the construction of trans-provincial joint protection and management systems, strengthening joint monitoring, joint law enforcement, and information sharing capabilities, etc.. The study offers reference for basin integrated protection and management for other trans-provincial rivers in China.