Abstract: A variety of ionospheric disturbance phenomena could pose grave impacts on Global Navigation Satellite System (GNSS) augmentation. The existed works, mainly for mid-latitudes ionosphere condition, are insufficient in low-latitude area where various disturbances exist. A method is proposed for GNSS augmentation study from the perspective of reliability engineering system. Attempt is made to analyze different ionospheric perturbations with failure model and effect analysis (FMEA) method to show the serious impacts. Disturbance detection procedures are also assessed for its effectiveness in augmentation system. The results show the existing designs could not cope with complex ionospheric conditions in low-latitude area for irregularity detection and identification. More efforts had to be made for augmentation systems covering China areas.