The invention belongs to the field of power system dispatching, and provides a wind-light-water multi-energy complementary system flexibility demand quantification and coordinated optimization method, which comprises the following steps of: firstly, constructing a flexibility demand quantification method considering wind-light output uncertainty, dividing a wind-light output interval by adopting quantiles, generating an output scene set, and generating a wind-light output scene set; further calculating flexibility requirements in each scene; and on the basis of the flexibility demand quantitative index, constructing a water-wind-light complementary optimization scheduling model considering that the system flexibility is insufficient and the expectation is minimum, and realizing water-wind-light complementary optimization calculation. Based on an actual wind-light-water complementary system of a Yunnan power grid, model verification is carried out for different new energy access proportions, and the result shows that the method can provide a multi-type power supply complementary operation scheduling scheme under different conditions, so that the flexibility requirement of the system is effectively met, the abandoned power quantity is reduced, and the consumption level of clean energy is improved.