Terahertz time-of-flight (THz-TOF) method is a new development direction in the field of thickness measurement, which has the advantages of fast, non-destructive and high precision. However, the water vapor in atmospheric environment has strong absorption of terahertz wave, which limits the application of THz-TOF method in atmospheric environment. The propagation mechanism of terahertz wave in atmospheric environment in THz-TOF method was firstly analyzed, and then a method of water vapor elimination based on absorption model was proposed. Finally, two kinds of plastic plate samples were used as the object of application research. By comparing with the measurement results in dry environment, the results show that the method can effectively eliminate the interference of water vapor and realize the accurate measurement of material thickness and refractive index in atmospheric environment.