BackgroundStructural variations (SVs) refer to variations in an organism’s chromosome structure that exceed a length of 50 base pairs. They play a significant role in genetic diseases and evolutionary mechanisms. While long-read sequencing technology has led to the development of numerous SV caller methods, their performance results have been suboptimal. Researchers have observed that current SV callers often miss true SVs and generate many false SVs, especially in repetitive regions and areas with multi-allelic SVs. These errors are due to the messy alignments of long-read data, which are affected by their high error rate. Therefore, there is a need for a more accurate SV caller method.ResultWe propose a new method-SVcnn, a more accurate deep learning-based method for detecting SVs by using long-read sequencing data. We run SVcnn and other SV callers in three real datasets and find that SVcnn improves the F1-score by 2–8% compared with the second-best method when the read depth is greater than 5×. More importantly, SVcnn has better performance for detecting multi-allelic SVs.ConclusionsSVcnn is an accurate deep learning-based method to detect SVs. The program is available athttps://github.com/nwpuzhengyan/SVcnn.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12859-023-05324-x.