As the accuracy requirements are approaching to millimeter level on GNSS applications like real-time troposphere zenith wet delay (ZWD) estimation, the higher-order ionospheric delays on GNSS signals are no longer negligible. In this research, the second-order ionospheric delays ( I 2 ) were calculated to analyze their impact on troposphere ZWD estimation with GPS-only and GPS/BeiDou integrated observations. On the troposphere ZWD estimation, the un-differenced PPP model with fixed coordinate was used to estimate troposphere ZWD, horizontal gradients as well as receiver clock biases. The block-wise sequential least square method was used to eliminate the clock biases in the estimation, and then the I 2 impacts on troposphere ZWD parameters were calculated every epoch with previous 30 minutes satellite observations. The high ionosphere TEC data on 29 th , Feb. 2016 from 11 IGS station around Asia-Oceania area were used on the research. The I 2 delays on each GNSS satellite observations were calculated with IGS final TEC map and the 12 th generation of international geomagnetic reference field (IGRF-12) model. The statistic results show that the I 2 delays on GNSS signals could reach up to over 10 millimeters on the daytime, and the corresponding impacts on troposphere ZWD estimation went up to millimeters level. The 24 hours statistic results show that the impact of the ZWD estimation is non-zero mean values, and the maximum values came from HKWS station (Hong Kong), the GPS only estimation reach up to 3.1 millimeters, and the maximum value decreased to 2.4 millimeters with GPS and BeiDou integrated observation. However, the I 2 impacts time series also show that the GPS/BeiDou integrated results are not necessarily smaller than GPS only estimation, which means that multi-GNSS may not always help decreasing the I 2 errors. In this research, the TEC and geomagnetic values are calculated from background models which are relative moderate than the real situation, but we still get millimeters levels difference on troposphere ZWD estimation. Compare to 5~10 millimeters accuracy on the real-time ZWD estimation, the I 2 delays impact should not be ignored. Hence, the I 2 delays should be corrected if more accuracy ZWD estimation is needed.