Non-negative Matrix Factorization (NMF) has been an ideal tool for machine learning. Non-negative Matrix Tri-Factorization (NMTF) is a generalization of NMF that incorporates a third non-negative factorization matrix, and has shown impressive clustering performance by imposing simultaneous orthogonality constraints on both sample and feature spaces. However, the performance of NMTF dramatically degrades if the data are contaminated with noises and outliers. Furthermore, the high-order geometric information is rarely considered. In this paper, a Robust NMTF with Dual Hyper-graph regularization (namely RDHNMTF) is introduced. Firstly, to enhance the robustness of NMTF, an improvement is made by utilizing the l_2,1-norm to evaluate the reconstruction error. Secondly, a dual hyper-graph is established to uncover the higher-order inherent information within sample space and feature spaces for clustering. Furthermore, an alternating iteration algorithm is devised, and its convergence is thoroughly analyzed. Additionally, computational complexity is analyzed among comparison algorithms. The effectiveness of RDHNMTF is verified by benchmarking against ten cutting-edge algorithms across seven datasets corrupted with four types of noise.