Non-coding RNAs (ncRNAs) play an important role in revealing the mechanism of human disease for anti-tumor and anti-virus substances. Detecting subcellular locations of ncRNAs is a necessary way to study ncRNA. Traditional biochemical methods are time-consuming and labor-intensive, and computational-based methods can help detect the location of ncRNAs on a large scale. However, many models did not consider the correlation information among multiple subcellular localizations of ncRNAs. This study proposes a radial basis function neural network based on shared subspace learning (RBFNN-SSL), which extract shared structures in multi-labels. To evaluate performance, our classifier is tested on three ncRNA datasets. Our model achieves better performance in experimental results. © 2022 The Author(s)