Nowadays, the localization and identification of acoustic emission (AE) source is widely utilized to structural health monitoring (SHM) of complex metallic structures. However, traditional AE source localization methods are generally difficult to localize and characterize AE sources in plate-like structure that has complex geometric features. To alleviate the problem, a novel AE source localization method based on all-phase fast Fourier transform and multiple cross-correlation analysis is proposed in this article. Moreover, least squares and Geiger iteration algorithm are applied to determine the coordinates of AE sources. In addition, an improved Bayesian information criterion (BIC) version named autoregressive BIC (i.e., AR-BIC) is presented to increase the accuracy of source localization. To validate the performance of the proposed approach, the classical pencil lead break tests are carried out on a 316 L stainless steel with 10 laser cladding layers. Experimental waveforms are generated from AE sources near laser cladding layers, the surface of the structure, and on its edges. Additionally, to evaluate the performance of the proposed approach in three-dimensional AE source localization, an industrial storage tank is used to acquire three-dimensional AE sources through manually striking. Finally, to further verify the effectiveness of the proposed approach, comparisons with conventional AE source location methods (i.e., PAC or SAMOS AE acquisition system, Newton’s method, and multiple cross-correlation based on Geiger algorithm) and two representative approaches (i.e., deep learning and Bayesian methodology) for localizing AE sources generated by complex metallic structures are conducted. The comparative results demonstrate the effectiveness and superiority of the proposed method in AE-based SHM of complex metallic structures.