Thermal barrier coatings (TBCs) exhibit excellent thermal insulation capabilities, proving crucial in enhancing the performance of turbine blades. Accurate measurement of TBC thickness is pivotal for the quality control and health monitoring of turbine blades. However, the absence of suitable non-destructive testing (NDT) methods poses a challenge in ensuring precise quality control and health assessment of TBCs. This study investigates the efficacy of terahertz time-domain spectroscopy (THz-TDS) in measuring TBCs thickness, specifically focusing on the microstructure characteristics of the top coat (TC), including grain morphology, internal porosity, surface roughness, and agglomerates. The findings emphasize the significance of grain morphology in determining thickness measurement due to the varied terahertz wave propagation modes. Moreover, the study involved polishing EB-PVD and APS samples to mitigate surface roughness. This process revealed a discernible linear correlation between reduced surface roughness and decreased measurement errors. The slopes of the error reduction curves ranged from 0.59 to 1.7 for EB-PVD and 2.17 to 5.79 for APS samples. Furthermore, the research observed THz light scattering within internal pores, resulting in diminished outgoing energies and subsequent increments in measurement errors.