Global navigation satellite system (GNSS) provides users with all-weather, continuous, high-precision positioning, navigation, and timing (PNT) services. In the operation and use of GNSS, the influence of the space environment is a factor that must be considered. For example, during geomagnetic storms, a series of changes in the Earth’s magnetosphere, ionosphere, and upper atmosphere affect GNSS’s positioning performance. To investigate the positioning performance of global satellite navigation systems during geomagnetic storms, this study selected three geomagnetic storm events that occurred from September to December 2023. Utilizing the global positioning system (GPS)/Beidou navigation satellite system (BDS) dual-system, kinematic precise point positioning (PPP) experiments were conducted, and the raw observational data from 100 stations worldwide was analyzed. The experimental results show that the positioning accuracy of some stations in high-latitude areas decreases significantly when using the conventional Geometry Free (GF) cycle-slip detection threshold during geomagnetic storms, which means that the GF is no longer applicable to high-precision positioning services. Meanwhile, there is no significant change in the satellite signal strengths received at the stations during the period of the decrease in positioning accuracy. Analyzing the cycle-slip rates for stations where abnormal accuracy occurred, it was observed that stations experiencing a significant decline in positioning accuracy exhibited serious cycle-slip misjudgments. To improve the kinematic PPP accuracy during magnetic storms, this paper proposes an adaptive threshold for cycle-slip detection and designs five experimental strategies. After using the GF adaptive threshold, the station positioning accuracy improved significantly. It achieved the accuracy level of the quiet period, while the cycle-slip incidence reached the average level. During magnetic storms, the ionosphere changes rapidly, and the use of the traditional GF constant threshold will cause serious cycle-slip misjudgments, which makes the dynamic accuracy in high latitude areas and some mid-latitude areas uncommon, while the use of the GF adaptive threshold can alleviate this phenomenon and improve the positioning accuracy in the high-latitude regions and some of the affected mid-latitude areas during the magnetic storms.