Three optimization models of inter-regional generation scheduling including clean energy generation, taking minimum regional generation cost, and minimum regional carbon emission cost and minimum comprehensive cost as objective functions respectively, were established, and the models considered the issues of economic efficiency, carbon emission, and transmission constraints. The simulation analysis using general algebraic modeling system(GAMS) shows that, (a) the model presented can optimize the inter-regional generation cost and environmental cost to a certain extent; (b) clean energy plays a more important role in the optimization of inter-regional energy allocation than fossil fuel energy by comparing the results of inter-regional energy allocation optimization with and without clean energy generation; and (c) the difference of carbon emission prices in regions will influence the benefit achieved by the energy replacement of clean energy and fossil fuel energy.