The problem of accurate source localization has been an area of focus in high-frequency surface wave radar (HFSWR) applications. However, antenna pattern distortion (APD) decreases the direction-of-arrival (DOA) estimation performance of the multiple signal classification (MUSIC) algorithm. Up to now, limited studies have been conducted on the calibration of antenna pattern distortion for phased arrays in HFSWR. In this paper, we first analyze the effect of APD on the performance of the MUSIC algorithm through estimation of accuracy and angular resolution. We demonstrate that using the actual pattern (or say APD) can improve DOA estimation performance. Based on this proposition, we propose a novel iterative calibration method that employs the first-order sea clutter data and can jointly estimate DOA and APD in an iterative way. To obtain available calibration points, we introduce the extraction methods of the first-order sea clutter spectrum and single-DOA spectrum points. Meanwhile, in each iteration, the Beamspace MUSIC algorithm and artificial hummingbird algorithm (AHA) are utilized to estimate the DOA and APD, respectively. Numerical results reveal a good coincidence between the actual pattern and the estimated APD. We also apply this method to process the experimental data of HFSWR. We obtain the APD vector of the real phased array and improve the direction-finding performance of several real ship targets using this vector. Both numerical and experimental results prove the correctness of our proposed calibration method.