In order to optimize the capacity configuration scheme for a hydro-photovoltaic complementary clean energy base, a comprehensive evaluation index system was constructed by selecting 14 indicators from the 4 aspects of safety, environmental protection, economy, and technology. An improved cloud model method was used to evaluate the capacity configuration scheme. The improved cloud model based on analytic hierarchy process was used to solve the subjective weights, the entropy weight method was used to solve the objective weights, the combined weighting was used to obtain the indicator weights, and then a conditional cloud generator was used to calculate the membership degree of each indicator. Finally, based on the level eigenvalue method, the capacity scheme rating was calculated to determine the optimal scheme. The method was applied to the optimization of the capacity configuration scheme for a hydro-photovoltaic complementary clean energy base in Southwestern China. The optimization results are consistent with the set pair analysis method and the actual selection scheme, proving the effectiveness and applicability of the method.