The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA–protein interactions and deciphering their mechanisms. In this chapter, we aim to introduce the fundamental framework for predicting lncRNA–protein interactions based on three-dimensional structure information. With the increasing availability of lncRNA and protein molecular tertiary structures, the feasibility of using deep learning methods for automatic representation and learning has become evident. This chapter outlines the key steps in predicting lncRNA–protein interactions using deep learning, including three common non-Euclidean data representations for lncRNA and proteins, as well as neural networks tailored to these specific data characteristics. We also highlight the advantages and challenges of structure-based prediction of lncRNA–protein interactions with geometric deep learning methods.