In this paper, we are interested in an efficient numerical method for the mixed-dimensional approach to modeling single-phase flow in fractured porous media. The model introduces fractures and their intersections as lower-dimensional structures, and the mortar variable is used for flow coupling between the matrix and fractures. We consider a stable mixed finite element discretization of the problem, which results in a parameter-dependent linear system. For this, we develop block preconditioners based on the well-posedness of the discretization choice. The preconditioned iterative method demonstrates robustness with regard to discretization and physical parameters. The analytical results are verified on several examples of fracture network configurations, and notable results in reduction of number of iterations and computational time are obtained.