Geothermal desalination is one of renewable energy-driven desalination technologies. Due to the continuous decrease of geothermal fluid temperature, desalination rate changes with running of the system. Therefore, this paper presents a theoretical study on the transient performance of geothermal desalination with variable geothermal fluid temperature. Firstly, a comprehensive model coupling with transient geothermal extraction and heat and mass transfer in desalination unit was built to simulate the transient performance. Deep coaxial borehole heat exchanger is used for geothermal extraction and humidification-dehumidification unit is taken for thermal desalination. Then the transient performances of the system, freshwater production rate, geothermal fluid temperature and extraction were studied and the effects on the transient performances were also investigated. The simulation results show that freshwater production rate drops by about 60 % during 20-years operation with continuous declination of geothermal fluid temperature and extraction, and the drop trend is strengthened with BHE depth and geothermal gradient rising, but weakened with increase of rock thermal conductivity. The production rate increases with air flow rate rising but decreases with increase of seawater flow rate. Both production rate and humidifying capacity can be enhanced by improving air temperature at inlet of humidifier and reducing the inlet relative humidity.