Atmospheric water vapour is an important contributor to global energy and water cycles and its detection is necessary for precipitation forecasting and climate change research. To explore the applicability of reanalysis data for determining precipitable water vapour (PWV) content in the Tarim Basin, China, this study compared the reliability of two reanalysis PWV products, ERA-5 (PWERA) and MERRA-2 (PWMER), using data from four ground-based global navigation satellite system stations representing basin ecosystems (Oasis, Gobi Desert, Central Desert, and Alpine; dataset: PWGNSS) as reference values. We conducted correlation analysis between PWGNSS and both reanalysis PWV products at different time scales to verify the products’ accuracy. The results showed that the reanalysis PWV products were mostly overestimated at the Desert station, while they were mostly underestimated at the Oasis station. The applicability of PWERA and PWMER varied by season and location, with better applicability at the Oasis station from spring to autumn. The applicability of reanalysis PWV products was lower during precipitation periods than during non-precipitation, and varied by location. During non-precipitation situation, the PWMER had better applicability at the Oasis station and at the Central Desert station when the PWGNSS exceeded 25 mm. Meanwhile, PWERA had better applicability in precipitation situation at the Gobi Desert station from April to June and at Oasis station from August to September when PWGNSS was above 30 mm, at the Central Desert station from May to August, and when the PWGNSS exceeded 30 mm.