The pseudopotential lattice Boltzmann (LB) method has been widely used for simulating multiphase flow due to its concise concept and computational simplicity. In this paper, based on the weighted orthogonal transformation matrix, a three-dimensional (3D) weighted multiple-relaxation-time pseudopotential lattice Boltzmann method (WRMT-LBM) is developed, in which the standard lattice stencil D3Q19 is adopted. Compared with the classical multiple-relaxation-time pseudopotential lattice Boltzmann method (CMRT-LBM) based on the orthogonal transformation matrix, the expressions of the equilibrium density distribution function and discrete force term in moment space are simplified in the present model, which contributes to simplifying the program implementation and improving the computational efficiency. Moreover, an additional discrete source term in moment space compatible with the proposed model is introduced to achieve tunable surface tension. A series of numerical tests are then implemented to investigate the performance of the proposed model. Compared with the CMRT-LBM, the results of the present model can achieve lower spurious velocity and higher computational efficiency while keeping comparable accuracy. Furthermore, using the present model, three benchmark cases, including droplet oscillation, droplet impacting on wall and droplet impact on thin film, are performed to investigate the performance of this model. The numerical results are in good agreement with the analytical solutions or the empirical correlations in the literature, which demonstrates that the present model can simulate the multiphase flow with large density ratio.