Demand fluctuates in actual production. When manufacturers face demand under their maximum capacity, suspension shifts are crucial for cost reduction and on-time delivery. In this case, suspension shifts are needed to minimize idle time and prevent inventory buildup. Thus, it is essential to integrate suspension shifts with scheduling under an uncertain production environment. This paper addresses the two-stage hybrid flow shop scheduling problem (THFSP) with suspension shifts under uncertain processing times, aiming to minimize the weighted sum of earliness and tardiness. We develop a stochastic integer programming model and validate it using the Gurobi solver. Additionally, we propose a dual-space co-evolutionary biased random key genetic algorithm (DCE-BRKGA) with parallel evolution of solutions and scenarios. Considering decision-makers’ risk preferences, we use both average and pessimistic criteria for fitness evaluation, generating two types of solutions and scenario populations. Testing with 28 datasets, we use the value of the stochastic solution (VSS) and the expected value of perfect information (EVPI) to quantify benefits. Compared to the average scenario, the VSS shows that the proposed algorithm achieves additional value gains of 0.9% to 69.9%. Furthermore, the EVPI indicates that after eliminating uncertainty, the algorithm yields potential improvements of 2.4% to 20.3%. These findings indicate that DCE-BRKGA effectively supports varying decision-making risk preferences, providing robust solutions even without known processing time distributions.