The permittivity of lunar regolith is crucial for further processing and interpretation of radar data. The conventional hyperbolic fitting method ignores the antenna height and spacing and has a significant error at a shallow depth. For the new method that considers the layout of the antenna, the influencing factors have not been studied. In this paper, we studied the influence of the position of the hyperbola peak and time zero on the new method for permittivity derivation. The simulation results show that when the input errors of time zero, abscissa and ordinate of the hyperbolic peak are ±2 ns, ±0.02 m and ±0.2 ns respectively, the average errors of the calculated results by points within 1 m from the hyperbolic peak are 10.0%, 16.7% and 38.2%, respectively. To improve the accuracy, we used the average results by points that are horizontally more than 1 m away from the hyperbola peak. Hence, we calculated the permittivity of the lunar regolith by the new method based on Lunar Penetrating Radar data. The average permittivity of the lunar regolith is estimated to be 3.3 ± 1.2.