Focusing on the problem that the cross-docking operation needs the decrease of the operation time in the distribution center as much as possible, considering the equivalent relationship between the total operation time and the longest operation time of the commodity supply, the paper sets up a model of dock door assignment problem in the distribution center, with the objective of minimizing the total operation time. We design a genetic algorithm to solve the problem, in which each individual is divided into two sections to do encoding, crossover and mutation operation. The results of experiment show that the model and algorithm can optimize the operation time in the distribution center effectively.