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• A 3D non-orthogonal MRT lattice Boltzmann model is developed for multiphase flows. • The Chapman-Enskog analysis justifies that the model recovers the Navier-Stokes equations. • The numerical accuracy of orthogonal MRT model is retained with simpler implementation. In the classical multiple-relaxation-time (MRT) lattice Boltzmann (LB) method, the transformation matrix is formed by constructing a set of orthogonal basis vectors. In this paper, a theoretical and numerical study is performed to investigate the capability and efficiency of a non-orthogonal MRT-LB model for simulating multiphase flows. First, a three-dimensional non-orthogonal MRT-LB is proposed. A non-orthogonal MRT collision operator is devised based on a set of non-orthogonal basis vectors, through which the transformation matrix and its inverse matrix are considerably simplified as compared with those of an orthogonal MRT collision operator. Furthermore, through the Chapman-Enskog analysis, it is theoretically demonstrated that the three-dimensional non-orthogonal MRT-LB model can correctly recover the macroscopic equations at the Navier-Stokes level in the low Mach number limit. Numerical comparisons between the non-orthogonal MRT-LB model and the usual orthogonal MRT-LB model are made by simulating multiphase flows on the basis of the pseudopotential multiphase LB approach. The numerical results show that, in comparison with the usual orthogonal MRT-LB model, the non-orthogonal MRT-LB model can retain the numerical accuracy while simplifying the implementation. [ABSTRACT FROM AUTHOR]