The flying foxes optimization (FFO) algorithm stimulated by the strategy used by flying foxes for subsistence in heat wave environments has shown good performance in the single-objective domain. Aiming to explore the effectiveness and benefits of the subsistence strategy used by flying foxes in solving optimization challenges involving multiple objectives, this research proposes a decomposition-based multi-objective flying foxes optimization algorithm (MOEA/D-FFO). It exhibits a great population management strategy, which mainly includes the following features. (1) In order to improve the exploration effectiveness of the flying fox population, a new offspring generation mechanism is introduced to improve the efficiency of exploration of peripheral space by flying fox populations. (2) A new population updating approach is proposed to adjust the neighbor matrices to the corresponding flying fox individuals using the new offspring, with the aim of enhancing the rate of convergence in the population. Through comparison experiments with classical algorithms (MOEA/D, NSGA-II, IBEA) and cutting-edge algorithms (MOEA/D-DYTS, MOEA/D-UR), MOEA/D-FFO achieves more than 11 best results. In addition, the experimental results under different population sizes show that the proposed algorithm is highly adaptable and has good application prospects in optimization problems for engineering applications.