Shore-based phased-array HF radars have been widely used for remotely sensing ocean surface current, wave, and wind around the world. However, phase uncertainties, especially phase distortions, in receiving elements significantly degrade the performance of beam forming and direction-of-arrival (DOA) estimation for phased-array HF radar. To address this problem, the conventional array signal model is modified by adding a direction-based phase error matrix. Subsequently, an array phase manifold calibration method using antenna responses of incoming ship echoes is proposed. Later, an assessment on the proposed array calibration method is made based on the DOA estimations and current measurements that are obtained from the datasets that were collected with a multi-frequency HF (MHF) radar. MHF radar-estimated DOAs using three calibration strategies are compared with the ship directions that are provided by an Automatic Identification System (AIS). Additionally, comparisons between the MHF radar-derived currents while using three calibration strategies and Acoustic Doppler Current Profilers (ADCP)-measured currents are made. The results indicate that the proposed array calibration method is effective in DOA estimation and current measurement for phased-array HF radars, especially in the phase distortion situation.