To increase the flexibility of power generation, the supercritical once-through boiler combined heat and power (CHP) plant should improve its coordinated control system (CCS). The difficulty of CCS for supercritical once-through boiler unit is to determine the water-fuel ratio in the dynamic process. First, a CHP unit model is established and simplified into a three-input three-output object under pure condensing working conditions. Second, dynamic relative matrix gain method and simulation is used to analysis several once-through boiler coordinated control schemes commonly used in engineering in which the compensation link is designed on the basis of water-fuel ratio. Simulation results show that, the water following CCS scheme has better intermediate point temperature performance and worse throttle pressure performance than the fuel following CCS scheme. To improve pressure performance, the closed-loop characteristics of pressure response to fuel and feed water flow are analyzed and compared through wavelet analysis. Finally, a method for determining the inertia time constant in the dynamic compensation link by comparing the wavelet coefficients is proposed. Wavelet analysis show that the imbalance in the speed of energy changes to fuel and feed water flow is the essential cause of large fluctuations in intermediate point temperature and throttle pressure before turbine of the supercritical once-through boiler unit. Simulation results show that using the proposed dynamic compensation in water following CCS can effectively reduce fluctuations of the intermediate point temperature and fluctuations of throttle pressure before turbine when power load command changes.