In recent years, the optimization of diesel engine exhaust mufflers has predominantly targeted acoustic performance, while the impact on engine power performance has often been overlooked. Therefore, this paper proposes a parallel perforated tube expansion muffler and conducts a numerical analysis of its acoustic and aerodynamic performance using the finite element method. Then, a Kriging model is established based on the Design of Experiments to reveal the impact of different parameter couplings on muffler performance. With transmission loss (TL) and pressure loss (PL) as the optimization objectives, a multi-objective optimization study is carried out using the competitive multi-objective particle swarm optimization (CMOPSO). The optimization results indicate that this method can simplify the optimization model and improve optimization efficiency. After CMOPSO calculation, the average TL of the muffler increased from 27.3 dB to 31.6 dB, and the PL decreased from 1087 Pa to 953 Pa, which reduced the exhaust noise and improved the fuel economy of the engine, thus enhancing the overall performance of the muffler. This work provides a reference and guidance for the optimal design of mufflers for small agricultural diesel engines.