The invention discloses a high-efficiency circuit topological structure evolution method and a system thereof. The high-efficiency circuit topological structure evolution method includes the steps: acircuit structure is converted into an initial population; a client performs selection and crossover operation on the initial population; one chromosome is randomly set as a chromosome to be mutated;the chromosome to be mutated is copied to form a replicated population, and mutation operation is performed on the replicated population, and the mutated chromosome with the maximum fitness value is retained in the initial population; and the chromosome with the maximum fitness value is obtained after the iteration operation on the initial population is completed to obtain a corresponding circuitstructure. Therefore, the variation efficiency is greatly improved, and the convergence speed is accelerated, and an optimal circuit structure is quickly and accurately obtained.