To address the multi-attribute, multi-level, and uncertain evaluation problem of capacity allocation schemes for hydro-photovoltaic complementary systems, a three-level evaluation index system covering five factor layers of security, environmental protection, economy, technicality, and sociality was constructed, and a comprehensive evaluation model based on combined weighting and cloud matter-element analysis method was proposed. In this model, subjective weights were determined through correction by the AHP-cloud model; objective weights were obtained by introducing the improved entropy weight method; weight fusion was realized based on Euclidean distance. Moreover, the cloud matter-element theory was applied to calculate the membership degrees of each scheme to evaluation grades and the comprehensive scores, expanding the grade boundaries from rigid thresholds to flexible distributions, thereby more reasonably depicting the random fluctuations and fuzzy transitions in the evaluation process. The results of the case verification for the clean energy base in the Xizang section of the Lancang River indicate that the model exhibits a good differentiation effect in the comparison and selection of multiple capacity allocation schemes. The evaluation results are consistent with the engineering operation characteristics, and the conflicts among multi-dimensional indicators can be effectively coordinated. The comprehensive evaluation model considers both the comprehensiveness of weight determination and the robustness of grade judgment, and it can provide scientific and reliable decision support for the capacity allocation of clean energy bases.