Modeling of vibro/acoustic systems with embedded acoustic components of complex geometries is a challenging task. In particular, the presence of irregular-shaped acoustic modules, which are usually treated by finite element (FE) method, increases system complexities and makes the use of existing sub-structuring modeling techniques cumbersome. To tackle the problem, an efficient three-dimensional sub-structuring modeling method is proposed in this paper. As an important sub-structural module, a dedicated coordinate transformation technique is established to cope with polygon acoustic components. The embodiment of the technique into the existing sub-structuring framework avoids the use of conventional FE modules, thus increasing the flexibility and the efficiency of the simulation, conducive to system optimization. As an example, noise reduction in a duct, comprising a Micro-Perforated Panel (MPP) liner and a trapezoidal expansion chamber, is examined. The accuracy of the proposed model is firstly validated against both FE simulations and experiments. Numerical results uncover a dual hybrid sound reduction process, namely sound absorption of the MPP and wave reflection due to the geometry changes of the duct. Optimizations based on the proposed sub-structuring technique allow one to balance the hybrid reflective-absorptive effects through proper parameter tuning to maximize the sound attenuation within a prescribed frequency range.