To evaluate the performance of a muffler, in this study, we used the four-pole parameter theory as the measurement basis, developed a measurement configuration and solution strategy for transmission loss (TL) based on microphone-position switching, and actually applied it to the air filter assembly. To reduce the phase mismatch in the measurement process, the dual-microphone transfer function method was used to correct the frequency response function to reduce the measurement error caused by the phase mismatch. In this study, LabVIEW was used to develop an algorithm for calculating TL. A relatively simple muffler was employed to measure its TL under zero-flow conditions. The analytical results were then compared with those obtained from finite element analysis to verify the effectiveness of the proposed algorithm. However, the original TL measurement did not take the fluid velocity into account and was not consistent with the actual working condition of the muffler. In this study, the TL measurement of fluid velocity was considered, and the corresponding results were compared with the measurement results without taking flow velocity into account to analyze the impact of flow velocity on TL. Experimental results obtained under both no-flow and flow conditions revealed that airflow significantly reduced the TL of the Helmholtz resonator and shifted its resonance frequency toward higher frequencies. The single expansion chamber and the inlet extended expansion chamber increased the TL effect owing to the effect of flow rate. Only the resonant frequency of the inlet extended expansion chamber had different effects, and the TL effect at the resonant frequency decreased. The automotive muffler assembly actually tested in this study has multiple Helmholtz resonance cavities, each of which is used to deal with noise at a single frequency. The resonance behavior of the actual automotive muffler assembly differs from that of the simplified Helmholtz resonator model because of the square duct geometry, bend, and resonator configuration.