A conservative Grid ionospheric vertical delay error (GIVE) estimation would lead to conservative Protection levels (PLs) estimation and affects Satellitebased augmentation systems (SBAS) service performance. To reduce the margin in GIVE estimation, an improved spatial threat model is presented. A new parameter ofMinimum separation distance (MSD) is introduced. The new model is described with the MSD, Relative centroid metric (RCM) and fit radius as inputs. Ionospheric delay measurements during storms are used to construct the new spatial threat model. Simulation results show that, with the new model, there is at least 9.5% reduction in User ionospheric vertical delay errors (UIVEs), while the user ionospheric delay estimation errors can be bounded at the same time. Even on severe ionosphere disturbed days, at least 5% improvement of PLs (95%) could be achieved for more than 20% Conterminous united states (CONUS) area, leading to higher system service performance.