As critical hydraulic structures, rubber dams are widely applied with integrated functions of water retaining, landscape construction and ecological regulation. Rational type selection design is essential to optimize the structure of water filling and draining system, realize accurate and rapid inflation/deflation control of rubber dams and guarantee stable operation of projects. This paper discusses a novel system of “double functions for one controller” in rubber dams i. e. water filling and draining control system, elaborates equipment selection, layout form and operational control scheme of the system. The proposed design simplifies operation and management mode, achieves coordinated optimization of project economy and management efficiency via innovative structural principle, reduces construction investment, and provides reference for similar projects.