This paper considers a bi-objective hybrid flowshop scheduling problems with fuzzy tasks’ operation times, due dates and sequence-dependent setup times. To solve this problem, we propose a bi-level algorithm to minimize two criteria, namely makespan, and sum of the earliness and tardiness, simultaneously. In the first level, the population will be decomposed into several sub-populations in parallel and each sub-population is designed for a scalar bi-objective. In the second level, non-dominant solutions obtained from sub-population bi-objective random key genetic algorithm (SBG) in the first level will be unified as one big population. In the second level, for improving the Pareto-front obtained by SBG, based on the search in Pareto space concept, a particle swarm optimization (PSO) is proposed. We use a defuzzification function to rank the Bell-shaped fuzzy numbers. The non-dominated sets obtained from each of levels and an algorithm presented previously in literature are compared. The computational results showed that PSO performs better than others and obtained superior results.