A new multiscale method combined with model order reduction is proposed for flow problems in three-scale porous media. We derive an effective three-scale model that couples a macroscopic Darcy equation, a mesoscopic Stokes-Brinkman equation, and a microscopic Stokes equation. A corresponding three-scale numerical method is then derived using the finite element discretization with numerical quadrature, where the macroscopic and mesoscopic permeability is upscaled at quadrature points from mesoscopic and microscopic problems, respectively. The computational cost of solving numerous mesoscopic and microscopic flow problems is further reduced by applying a Petrov–Galerkin reduced basis method at the mesocopic and microscopic scales. As there is no natural way to obtain an affine decomposition of the mesoscopic problems, which is instrumental for the efficiency of the model order reduction, we derive a mesoscopic solver that makes use of empirical interpolation techniques. A priori and a posteriori error estimates are derived for the new method that is also tested numerically to corroborate the theoretical convergence rates and illustrate its efficiency.