Abstract Motivation Molecular property prediction (MPP) is a fundamental but challenging task in the computer-aided drug discovery process. More and more recent works employ different graph-based models for MPP, which have achieved considerable progress in improving prediction performance. However, current models often ignore relationships between molecules, which could be also helpful for MPP. Results For this sake, in this article we propose a graph structure learning (GSL) based MPP approach, called GSL-MPP. Specifically, we first apply graph neural network (GNN) over molecular graphs to extract molecular representations. Then, with molecular fingerprints, we construct a molecule similarity graph (MSG). Following that, we conduct GSL on the MSG, i.e. molecule-level GSL, to get the final molecular embeddings, which are the results of fuzing both GNN encoded molecular representations and the relationships among molecules. That is, combining both intra-molecule and inter-molecule information. Finally, we use these molecular embeddings to perform MPP. Extensive experiments on 10 various benchmark datasets show that our method could achieve state-of-the-art performance in most cases, especially on classification tasks. Further visualization studies also demonstrate the good molecular representations of our method. Availability and implementation Source code is available at https://github.com/zby961104/GSL-MPP.