To adapt to the uncertainty of the real environment and solve the problem of high efficiency and high quality, this study comprehensively considers a variety of uncertainty factors, focusing on modeling and solving a hybrid flow-shop scheduling problem by two-stage stochastic programming (HFSP-TSP). First, this paper uses a two-stage scenario tree to describe the uncertain factors, the probabilities and values are obtained under different discrete production scenarios, and stochastic programming theory is used to formulate a mixed-integer linear programming (MILP) model for HFSP-TSP. Second, based on a general discrete optimization algorithm framework, that is, pointer-based discrete differential evolution (PDDE) algorithm, a novel variant (H-PDDE) is proposed for effectively solving the HFSP-TSP. It adopts a permutation scheduling decoding method and introduces three new improvement strategies: the strategy of inconsistent code length of individuals in the population, adding local search in discrete mutation operation, using a heuristic algorithm to generate the initial population. Finally, computational experiments were conducted to illustrate the proposed mathematical model and optimization algorithm. The computational results show that the H-PDDE can solve the HFSP-TSP more effectively than existing algorithms and conventional PDDE variants. The stochastic programming model is increasingly superior to the deterministic model in an uncertain environment. The source code of the H-PDDE algorithm and its data files can be found at https://github.com/huangyiping-ai/H-PDDE-algorithm.git, which is publicly available.