Abstract: Traditional boresight error measurement methods require the antenna phase center of the phased array radar to align with the rotation center of the three-axis turntable within the designated coordinate system. The paper relaxes this constraint and proposes a generalized methodology for boresight error measurement under non-coincident conditions between the radar antenna’s phase center and the turntable’s mechanical rotation center, applicable to both near-field and far-field scenarios. It establishes a unified quaternion-based framework for the first systematic theoretical derivation of boresight errors under multi-source perturbations, including lever-arm error, feed antenna position calibration uncertainties, and radar installation attitude angle deviations. A comprehensive theoretical analysis is performed to quantify the contributions of multiple error sources to boresight error measurement in phased array radar systems. Both numerical simulation results and field measurement data form practical engineering applications validate the effectiveness of the proposed methodology, demonstrating its practical guiding significance for real-world engineering implementations.