The invention discloses a wind power, hydraulic power and thermal power generating unit optimizing and coordinating method and system. The method comprises, firstly, according to the current starting and stopping plan of generating units and short-term and ultrashort-term wind power predication, determining the total second-level standby requirements of a regional power grid; secondly, performing optimization combined computation on hydraulic power generating units and thermal power generating units in the regional power grid; thirdly, according to output limits of the generating units, determining and checking whether second-level standby capacity requirements reach a designated second-level standby capacity, and if not, adjusting the output limits of the generating units with second-level standby abilities; fourthly, performing simulating calculation on generating unit combination schemes meeting the second-level standby capacity requirements to check whether the second-level standby capacity can maintain the frequency at a designated level when wind power generating output changes within a designated range. The wind power, hydraulic power and thermal power generating unit optimizing and coordinating method can achieve generating unit combined optimization according to the characteristics of hydraulic power, thermal power and gas generating units to determine necessary second-level standby, meet the load requirements and minimize the operating cost of the entire system.