This paper presents an application of synergy methodology to a multiobjective operational control of reservoirs. This methodology enables a comprehensive consideration of multi-objectives which may be conflicting and non commensurate such as municipal and industrial water supply, flood protection, and hydroelectric power generation etc. On the basis of the synergy theory, a harmony degree model of subsystem was established to describe the coordination magnitude. Combined with information entropy, a harmony degree entropy was proposed to determine the water resources evolvement direction. While implementing the control, an initial scheme for reservoir operation was obtained from simulation first, then control was carried out according to the harmony degree and harmony degree entropy by applying synergy theory. The application of the methodology to reservoir system in the Yellow River was reported in this paper through a case study.