This paper analyzes the process of single operation and compound operation of AS/RS, according to the characteristics of compound operation, constructs an optimized mathematical model based on minimal operating time, and then proposes an effective genetic algorithm to solve the combinatorial sequence of compound operations. Case studies demonstrate the effectiveness of the algorithm for compound operation optimization problem of AS/RS, which can obtain a better optimal solution in a smaller initial population, reduce the operating time of stacker and improve the working efficiency of ASIRS.