The distributed assembly hybrid flow shop scheduling problem (DAHFSP) is a type of distributed shop scheduling problem, and each distributed shop can be regarded as a hybrid flow shop. In distributed assembly processes for complex products such as satellites and missiles, transportation time and worker assignment have important effects on production scheduling. Based on real production situations, this study proposes a novel DAHFSP considering worker assignment and transportation time, aiming to minimise the makespan and the imbalance degree of worker workloads. First, to solve these problems, we construct a mathematical model and design a two-layer chromosome coding scheme including worker assignment and task sequence. Then, in the local search stage, we propose a mutation-based search method and an elite search method. On that basis, we propose a multi-objective evolutionary algorithm with reinforced elite retention strategy (MOEA-RERS). Finally, based on a set of 12 test instances generated by actual enterprise production data, we compare the MOEA-RERS algorithm with five multi-objective evolutionary algorithms. The results show that the MOEA-RERS algorithm is superior to other algorithms in terms of solution quality and distribution.