To address the uneven spatial-temporal distribution of water resources and the intensifying contradiction between water supply and demand in Yunnan Province under changing environments, a modern three-dimensional water network spatial pattern for Yunnan Province characterized by “one main region and four sub-regions, water transfer from west to east, three-dimensional allocation and multi-source mutual replenishment” is established with major water diversion and transfer projects as the backbone. The evaluation index system for water resources system resilience covering resistance, recovery, and adaptability was established. The projection pursuit model optimized by accelerated genetic algorithm was employed to compare and analyze the water resources system resilience in the benchmark year