To address the problem of severe performance degradation of the land-based augmentation system for satellite navigation under ionospheric storms, appropriate processing strategies, monitoring and positioning algorithms are proposed. A ground-space cooperative processing strategy is constructed to monitor ionospheric anomalies in real time by using the residual values of dual-frequency Divergence-Free Smoothing (D-Free); satellites are classified according to the results of anomaly monitoring and various dual-frequency filtering is performed; and a position monitoring model based on the Weighted Least Square (WLS) method is established to achieve optimal estimation of the system's position and protection level. Optimal estimation. The simulation results of typical scenarios show that: the accuracy of ionospheric anomaly monitoring based on dual-frequency D-Free residuals is better than the existing methods; the positioning method based on dual-frequency combination has no bias in positioning, and the accuracy and protection level become significantly smaller. The new method makes full use of all ground and airborne observation data for optimal estimation, which effectively improves the system integrity compared with the existing methods such as the D-free and Ionosphere-Free Smoothing (I-Free).