Nonnegative matrix factorization (NMF) is a widely recognized approach for data representation. When it comes to clustering, NMF fails to handle data points located in complex geometries, as each sample cluster is represented by a centroid. In this article, a novel multicentroid-based clustering method called graph-based multicentroid NMF (MCNMF) is proposed. Because the method constructs the neighborhood connection graph between data points and centroids, each data point is represented by adjacent centroids, which preserves the local geometric structure. Second, because the method constructs an undirected connected graph with centroids as nodes, in which the centroids are divided into different centroid clusters, a novel data clustering method based on MCNMF is proposed. In addition, the membership index matrix is reconstructed based on the obtained centroid clusters, which solves the problem of membership identification of the final sample. Extensive experiments conducted on synthetic datasets and real benchmark datasets illustrate the effectiveness of the proposed MCNMF method. Compared with single-centroid-based methods, the MCNMF can obtain the best experimental results.