The clean energy sources such as hydropower and wind power increase dramatically due to the non-renewable and environmental pollution of fossil energy, which also bring some new problems to the dispatching operation of the power system. To deal with the problem induced by the optimal operation of multi-source energy in a single period of day-ahead plan, we propose an optimal joint clearing model, which coupling the random variables of intermittent power sources and determinant variables of conventional power sources in a large multi-time scale including mid-long term, day-ahead, and real-time. Based on the joint clearing model, the example of multi-source power system from Fujian power grid is simulated, the outputs of multi-source units are well coordinated, where the complementary characteristics and benefits of multiple energy sources are achieved.