This study deals with the characterization of multilayer adhesive structures via terahertz waves, particularly focusing on inversion analysis of the adhesive layer thickness. Terahertz-time-of-flight (THz-TOF), sensitive to the dielectric properties of materials, serves as an excellent device for non-destructive evaluation. Further, the transfer matrix method is introduced to simulate THz propagation through layered materials with various optical properties. An improved model iteration approach and particle swarm optimization algorithm are employed to effectively determine the adhesive layer thickness. This methodology utilizes effective medium theory (EMT), specifically for adhesive penetration into the cushion, thereby enhancing the thickness measurement accuracy. Among the various EMT models, the Lorentz-Lorenz (L-L) model is commonly regarded as the most effective one. An objective function based on combining the Pearson correlation coefficient and the root mean square error is proposed to refine the iterative inversion process. The results of this approach have been benchmarked with traditional THz-TOF calculations and computed tomography imaging, revealing that the proposed methodology is consistent with CT findings and outperforms conventional THz-TOF calculations.