Paint thickness management has a significant impact on waterproofing, rust-proof function and color effects of products in the field of automotive, aircraft, ships, etc. However, commercially available coating thickness meters are contact-type, and it is difficult to determine the individual paint thickness for each layer of the multilayer coating directly. In this paper, the terahertz pulse waveforms of samples were detected with reflection terahertz time-domain spectroscopy (THz-TDS) system, and the simple single-point thickness measurement model was established based on the time-of-flight measurement of the pulse echo. Besides, the refractive indexes of 12 kinds of paint samples coated on aluminum panels were calculated from the linear relationship between the optical thickness and geometrical thickness, which was fitted by the least squares method. It was found that there was a big difference of refractive index between the metallic paint and nonmetallic paint in the terahertz band, and the measuring refractive index was 5.15 for shining silver paint and 2.64 for white paint. The thickness of monolayer white paint sample was measured by detecting the thickness of 50 points in the region that the thickness distribution was uniform, and the average value of thickness was 72 μm with an error of 4 μm when the reference standard was the data measured by the electromagnetic/eddy current thickness meter. By two-dimensional (2-D) scanning, the observed uniformity of the thickness distribution of two-layer paint sample was (233±13) μm for white paint and (130±11) μm for primer. Similarly, the individual paint thickness for each layer and the distribution uniformity of the three-layer paint black samples or silver samples was determined by analyzing the thickness 2-D map. The results showed that terahertz pulse spectroscopy provided a feasible method of measuring film thickness and assessing uniformity of 1~3 layer paint, and the method could provide a higher thickness resolution for metallic paint. It was easy to assess the quality of the multilayer paint with the thickness data and 2-D distribution information extracted from terahertz pulsed waveforms detected in non-contact way.