A multi-objective integer programming model is presented for the billet warehouse stacking optimization problem with the purpose of minimizing the stacking shuffles and the switches of rolling units. The optimization of billet warehouse stacking based on the given rolling plan is taken into consideration in the proposed model. To solve the model, a parthenogenetic algorithm based on the billet match is constructed. The experiment results from the real production data show that the algorithm improves 20% on average for optimizing the stacking shuffles and the switches of rolling units through comparing with the traditional manual method, which illustrates the effectiveness of the proposed model and algorithm.