Three-dimensional structure-based localization aims to estimate the six-DOF camera pose of a query image by means of feature matches against a 3D Structure-from-Motion (SfM) point cloud. For city-scale SfM point clouds with tens of millions of points, it becomes more and more difficult to disambiguate matches. Therefore, a 3D structure-based localization method, which can efficiently handle matches with very large outlier ratios, is needed. We propose a two-stage outlier filtering framework for city-scale localization that leverages both visibility and geometry intrinsics of the SfM point clouds. First, we propose a visibility-based outlier filter, which is based on a bipartite visibility graph, to filter outliers on a coarse level. Second, we apply a geometry-based outlier filter to generate a set of fine-grained matches with a novel data-driven geometrical constraint for efficient inlier evaluation. The proposed two-stage outlier filtering framework only relies on the intrinsic information of the SfM point cloud. It is thus widely applicable to be embedded into the existing localization approaches. The experimental results on two real-world datasets demonstrate the effectiveness of the proposed two-stage outlier filtering framework for city-scale localization.