The frequency domain interferometry (FDI) technique uses two or more frequencies to measure the positions and thicknesses of the atmospheric thin layers embedded in the radar volume, in which the cross-correlation analyses of the radar echoes for the pairs of carrier frequencies are performed and the resultant amplitudes and phases (FDI phase) are both employed. However, in light of the possibility that the characteristics of radar system, mean refractivity gradient, and other factors that would significantly affect the FDI phase, calibration of the FDI phase is required to improve the measurement. In this study we employed three methods in measuring the phase bias in the FDI observation using the Chung-Li VHF radar; namely, (1) histogram of the FDI phases, (2) relationship between echo power and FDI phase, and (3) the FDI phase of aircraft. Both methods 1 and 2 are based on the range weighting effect on the radar echoes returned from the atmospheric scatterers; however, the first produced smaller FDI phase bias than the second. To examine such discrepancy in the results of methods 1 and 2, method 3 was exploited and provided more consistent values of phase biases with those of method 2. Considering that the radar echoes reflected from aircrafts are not related to uncertain conditions of the atmosphere such as mean reflectivity gradients and statistical characteristics, the results of methods 2 and 3 may be more reliable. Besides, the first two methods demonstrated that the FDI phase bias was quasi-linearly dependent on the separation of frequency pair, which not only consolidates the existence of the FDI phase bias but also indicates that a systematic phase compensation for the FDI analysis is possible. For example, considering 0.1-, 0.4-, and 0.8-μs time delays of signals for the returns of 1-, 2-, and 4-μs pulse lengths, respectively, the FDI phase biases can be removed effectively. Same methods and procedures can be applied to other radar systems.