Air bubbles in seawater always lead to information loss for sub-bottom profiler (SBP) images. This common issue makes it difficult to interpret SBP data. Toward this end, this letter proposes a hybrid method to reconstruct the missing area on an SBP image. This method combines the information of multi-survey line to overcome the disadvantage of using a single survey line that has less observation information. First, based on an improved active contour model (ACM) algorithm and a bottom line match algorithm, the SBP images of adjacent survey lines are aligned, and the image patch group is obtained. Then, a multi-survey line patch group deep learning framework is trained to reconstruct the missing area using the patch group as the input layer. The global–local loss function is employed to optimize the deep learning training model. Both simulated and real experiments have been used to test the effectiveness of the proposed method, and good results have been achieved.