Transient electromagnetic (TEM) techniques have been proven to be efficient for nondestructive testing (NDT) operations due to their pulsed eddy-current properties. However, in the field of downhole measurements, harsh environments may significantly influence the NDT performance in downhole casings. In this paper, an empirical mode decomposition (EMD) method based on borehole TEM array signal denoising and baseline wander (BW) correction is proposed to compensate for the bad measurement conditions that affect downhole NDT. Based on the borehole TEM signal model, we investigated the principle of the EMD approach for the borehole TEM response, where the background magnetic noise and temperature drift effects were analyzed by considering the motion measurement and effective permeability. It was found out that although the BW can be effectively removed with the EMD approach, the performance of the signal denoising is closely related to the measurement speed of the downhole NDT sensors. To solve this problem, we proposed an array-based ensemble EMD method to improve the denoising performance of the borehole TEM signals by formulating a three-dimensional borehole TEM data structure, where the generation of the noise-aided data can be more efficient by employing the borehole TEM array. The performance of the proposed method was verified by applying it to a borehole TEM system for the NDTs of oil-well casings. In addition, field experiments were conducted, and the results demonstrated the effectiveness of the proposed method.