The hybrid flow shop scheduling problem (HFSP) is an extension of the classic flow shop scheduling problem and widely exists in real industrial production systems. In real production, sequence-dependent setup times (SDST) are very important and cannot be neglected. Therefore, this study focuses HFSP with SDST (HFSP-SDST) to minimize the makespan. To solve this problem, a mixed-integer linear programming (MILP) model to obtain the optimal solutions for small-scale instances is proposed. Given the NP-hard characteristics of HFSP-SDST, an improved artificial bee colony (IABC) algorithm is developed to efficiently solve large-sized instances. In IABC, permutation encoding is used and a hybrid representation that combines forward decoding and backward decoding methods is designed. To search for the solution space that is not included in the encoding and decoding, a problem-specific local search strategy is developed to enlarge the solution space. Experiments are conducted to evaluate the effectiveness of the MILP model and IABC. The results indicate that the proposed MILP model can find the optimal solutions for small-scale instances. The proposed IABC performs much better than the existing algorithms and improves 61 current best solutions of benchmark instances.