As we all know, science and technology are developing faster and faster. Many experts and scholars have demonstrated that human diseases are related to lncRNA, but only a few associations have been confirmed, and many unknown associations need to be found. In the process of finding associations, it takes a lot of time, so finding an efficient way to predict the associations between lncRNAs and diseases is particularly important. In this paper, we propose a multi-label fusion collaborative matrix factorization (MLFCMF) approach for predicting lncRNA-disease associations (LDAs). Firstly, the lncRNA space and disease space are optimized by multi-label to enhance the intrinsic link between lncRNA and disease and to tap potential information. Multi-label learning can encode a variety of data information from the sample space. Secondly, to learn multi-label information in the data space, the fusion method is used to handle the relationship between multiple labels. More comprehensive information will be obtained by weighing the effects of different labels. The addition of Gaussian interaction profile (GIP) kernel can increase the network similarity. Finally, the lncRNA-disease associations are predicted by the method of collaborative matrix factorization. The ten-fold cross-validation method is used to evaluate the MLFCMF method, and our method finally obtains an AUC value of 0.8612. Detailed analysis of ovarian cancer, colorectal cancer, and lung cancer in the simulation experiment results. So it can be seen that our method MLFCMF is an effective model for predicting lncRNA-disease associations.