Abstract: A new method is developed on analyzing and estimating phase differences between each antenna of All-sky meteor radar by the mathematical model derived from the distribution of meteors and the antenna configuration. Using the observational data collected from the meteor radar, the temporal-spatial distribution properties of meteors and their effect upon the spatial distribution of meteors, especially the effect upon the variance properties of height distribution result from the phase difference variations of the antennas, are achieved. On this basis a simulation is created to estimate the phase difference variations by the variance of meteors' height distribution. Then this method is applied to analyze data collected from Sanya All-sky meteor radar. The results show that phase difference variations from one antenna or more are able to be estimated by analyzing the observational data without any additional hardware. And the accuracy is less than 2 degree. The calibration to the phase different variations can efficiently improve the measurement precision of the meteors' angles of arrival and the relevant data quality.