The ionosphere plays a critical role in the electromagnetic waves in communication systems such as the global positioning system (GPS). However, it is suspected that the strong convection during the tropical cyclone (TC) events can be a trigger to anomalous electron density variation in the ionosphere. This study analyzed the variation of three ionosphere-related parameters based on the GPS data including scintillation index S4, cycle slips, and total electron content (TEC) rate (TECR) during the tropical cyclone event (the 2013 TC Usagi) in the Hong Kong region. The results showed that the ionosphere-related parameters had a consistent significant increase on the second day after the Usagi made landfall near Hong Kong. Consequently, the positioning performance of GPS precise point positioning (PPP) and relative positioning modes was degraded. The degradation was ~ 138%, ~ 181%, and ~ 460% in the east (root mean square (RMS) 0.050 m), north (RMS 0.045 m), and up (RMS 0.185 m), respectively, compared with the RMS of 0.021 m in the east, 0.016 m in the north, and 0.033 m in the up on the normal day. Regarding the relative positioning, the positioning errors in the east (RMS 0.134 m) and north (RMS 0.118 m) directions were ~ 7.1 and ~ 7.9 times, respectively, as large as the RMS of 0.019 m in the east and 0.015 m in the north on the normal day. The positioning errors in the up (RMS 0.513 m) direction were ~ 12.2 times larger than the RMS of 0.042 m on the normal day.