The calculation of the transmission loss of the silencers with complicated internal structures by the conventional BEM combined with the transfer matrix method is incorrect at best or impossible for 3-dimensional silencers due to its inherent plane wave assumption. On this consideration, we propose an efficient practical means to formulate algebraic overall condensed acoustic equations for the whole acoustic structure, where particle velocities on the domain interface boundaries are unknowns, and the solutions are used later to compute the overall transfer matrix elements, based on the multi-domain BEM data. The transmission loss estimation by the proposed method is tested by comparison with the experimental one on an air suction silencer with perforated internal structures installed in air compressors. The method shows its viability by presenting the reasonably consistent anticipation of the experimental result.