Efficient scheduling in flow shop environments with lot streaming remains a critical challenge in various industrial settings, necessitating innovative approaches to optimize production processes. This study investigates a hybrid flow shop scheduling problem dominant in real-world printed circuit board assembly shops. A novel multi-objective hyper-heuristic combining Q-learning, i.e., two-stage improved spider monkey optimization (TS-ISMO), is tailored to address the complexities of the flow shop scheduling problems. The proposed method aims to simultaneously optimize conflicting objectives such as minimizing makespan, total energy consumption, and total tardiness time while incorporating lot streaming considerations. For multi-objective hyper-heuristic techniques, the algorithm dynamically selects and adapts a diverse set of low-level heuristics to explore the solution space comprehensively and strike a balance among competing objectives. The proposed TS-ISMO algorithm incorporates several significant features aimed at enhancing its performance. These features encompass hybrid heuristics for solution initialization, a contribution value method for comprehensive convergence and diversity assessment, diverse evolutionary state judgments to promote the algorithm’s balance between exploration and exploitation capabilities, and a Q-learning strategy for self-adaptive parameter tuning. The integration of Q-learning facilitates intelligent parameter control, enabling the algorithm to autonomously adjust its behavior based on past experiences and evolution dynamics. This adaptive mechanism enhances convergence speed and solution quality by effectively guiding the search process toward promising regions of the solution space. Extensive computational experiments are conducted on benchmark instances of hybrid flow shop scheduling problems with lot streaming to evaluate the performance of the proposed algorithm. Comparative analyses against state-of-the-art approaches demonstrate its superior solution quality and computational efficiency.