The Dual Reciprocity Boundary Element Method (DRBEM) is applied to predict the acoustic characteristics of ducts and silencers with three-dimensional potential flow, and the basic principle and numerical procedure of the proposed method are introduced. Compared to the Conventional Boundary Element Method (CBEM), the DRBEM takes into account the second order terms of flow Mach number in the acoustic governing equation, which is suitable for the situations with higher Mach number subsonic flow. The four-pole parameters of a duct and a varying cross-sectional area expansion chamber are predicted with the DRBEM, and the predictions are compared with the one-dimensional analytical solutions and the CBEM results. The comparisons demonstrated that the present method is valid. Transmission loss of silencers with different structures was also calculated with the DRBEM. The results showed that the influence of the three-dimensional flow on the acoustic characteristics of silencers with complex structures is not negligible.