Abstract Two-sided production line can utilize both the left and right stations to increase the productivity of large-sized products. For the disassembly of large-sized waste products such as cars and buses, the two-sided layout is introduced into the disassembly line. This paper constructs a mathematical model of the stochastic two-sided partial disassembly line balancing with multi-objective, multi-constraint and uncertainty. The aim is to optimize the number of stations, workload smoothness, energy consumption and profit of the production line simultaneously. A multi-objective discrete flower pollination algorithm based on Pareto dominance relations is proposed as the optimization method of the problem. In order to improve the quality of initial solutions, four heuristic rules combining the characteristics of the problem are designed. The effectiveness of the heuristic rules and the superiority of the proposed algorithm are verified by solving a set of test problems, and the application capabilities of the proposed model and method have also been verified.