Abstract: An analysis with GPS data was conducted to identify the possible serious effects that special characteristics, including ionospheric anomaly, ionospheric storm and ionosphere scintillation existing in China area will have on system integrity and availability. The ionospheric anomaly could make the ionospheric delay less correlated to establish a reasonable threshold to bound ionospheric residual error. Breaking down the ionospheric correlation structure, an ionospheric storm will make it a more difficult work to derive an appropriate threshold and effective disturbance detection as well. Ionospheric scintillation could affect the system availability as it will cause errors in pseudo-range measurement, losing of available satellites under severe scintillation condition and finally an erroneous position fixing. Irregularity related to scintillation will also cause a bad estimation of TEC, resulting in difficulties in GNSS ionospheric correction model realization. All these effects often work on each other, making the things even worse.