The index system of the initial water rights allocation was constructed following the principle of effectiveness, equity and sustainability. Aiming at the problems of significant correlation of index system and inconsistency of weight preference of initial water rights allocation, Principle Component Analysis (PCA) was applied to the initial water rights allocation to eliminate the impact of correlation. In the method, firstly, Principle Component Analysis (PCA) was proposed to empower the index system, Thereafter, improved AHP and entropy method were adopted to determine weights for multi-lever index system, which eliminated the unilateral result. And game theory was used to carry out the comprehensive integration of index weight. Finally, a comprehensive evaluation method was used to allocate initial water rights. The method was applied to study the initial water rights allocation in Yingcheng, Hubei province. The verification of the model and the analysis of the experimental results showed that the proposed method worked well and was rational and practical. The model could provide a reference for initial water rights allocation in other areas and lay the foundation for the unity management of the water resources.