A new approach to analyze the multi-domain acoustic system divided and enclosed by flexible structures is presented in this paper. The boundary element formulation of the Helmholtz integral equation is used for the internal fields and the finite element formulation for the structures surrounding the fields. We developed a numerical analysis program for the structural-acoustic coupling problems of the multi-domain system, in which boundary conditions such as the continuity of normal particle velocity and sound pressure in the structural interfaces between Field 1 and Field 2 are not needed. The validity of the numerical analysis program is verified by comparing the numerical results with the experimental ones. Example problems are included to investigate the characteristics of the coupled multi-domain system.