The invention provides an operation optimization method of a complex parallel cascaded pump station system. The method comprises the following steps of: firstly, building a related optimization model, supposing that a dual-line cascaded pump station system comprises n cascaded levels of pump stations, connecting two water supply lines between the k level pump station (k = 1, 2,..., n) and the k+1 level pump station in parallel to mix the two water supply lines, and then, supplying water to a destination in two paths; and after the constraint conditions of water level, flow, pump unit head of delivery and number of pump stations to be turned on are satisfied, dispersing the to-be-optimized parameters in upper two layers by aiming at minimizing the total input power of the system pump stations and using a multilayer decomposition-dispersion method, namely, solving an in-station optimization scheme of the lower two layers by using a simulated annealing particle swarm optimization algorithm, calculating the total operation power of the whole parallel cascaded pump station system, and considering the in-station optimization scheme as the optimized operation scheme of the whole engineering system if the total operation power is lowest. The method provided by the invention can be used for operation optimization of large parallel cascaded pump stations, expectedly, can save energy by 3%-8%, makes full use of the efficiency of the pump stations, promotes establishment of harmonious society and has great social and economic benefits.