Ceramic adhesive structures have been increasingly used in aerospace applications. However, the peaks of the signal on the upper and lower surface of the adhesive layer are difficult to measure directly due to the thin thickness of the adhesive layer and the effect of the attenuation dispersion of the ceramic layer. Thus, the existing non-destructive testing techniques have been ineffective in detecting adhesive quality. In this paper, the thickness of the adhesive layer is measured using terahertz time-domain spectroscopy. A sparse deconvolution method is proposed for the terahertz time-domain spectral signal of ceramic adhesive structures with different adhesive layer thicknesses. The results show that the methods proposed in this paper can realize the separation of reflection signals for glue layers with a thickness of 0.20 mm. By comparing with a wavelet denoising method and a modified covariance method (AR/MCM), the effectiveness of the sparse deconvolution method in estimating the thickness of the glue layer is demonstrated. This work will provide the theoretical and experimental basis for using terahertz time-domain spectroscopy to detect the homogeneity of ceramic adhesive structures.