The array InSAR system obtains a three-dimensional image of an observed scene using a combination of pulse compression and synthetic and real aperture techniques. However, Antenna Phase Center (APC) errors can occur within a practical array InSAR system, which thus degrades the imaging quality in a height direction. The aim of this paper is to improve calibration problems occurring with APC errors. The effect of APC errors is analyzed, and a calibration method based on the orthogonal subspace principle is proposed that utilizes SAR Single Look Complex (SLC) to obtain the noise subspace through eigenvalue decomposition. The subspace orthogonal principle is then used to solve the APC positions of multiple channels simultaneously. In addition, a calibration scheme for the APC position is presented for application with an array InSAR system. The effectiveness of the proposed calibration method is verified using simulations and experimental results.