A new scheme was proposed in this article to estimate the system phase bias of the interferometry array of the Chung-Li VHF radar inherently induced by phase imbalance between defferent modules of the array. The system phase bias of the ionospheric array of the Chung-Li VHF radar specifically designed for the purpose of observing ionospheric electron density irregularities has been successfully calibrated by using the radar returns from highly field-aligned sporadic E (Es) irregularities incorporating with IGRF95 model. These irregularities can be affected by space weather events through changes of the global electric field. By comparing the angles of arrival of the Es echoes received simultaneously by ionosphere and interferometer arrays, the system phase biases of interferometer array are determined. The results show that the phase bias is about 66° between receiving channels 1 and 2, and is about 56° between receiving channels 3 and 2. Once the interferometer array is well calibrated, the locations of meteor echoes in the scattering volume can thus be determined accurately.