Knowledge of water use efficiency (WUE) at the ecosystem level is imperative as it is a critical ecophysiological index reflecting the coupling processes between carbon sequestration and water consumption. However, the temporal patterns of WUE and their underlying regulating factors during different seasons in tea plantations, which are under intense pruning practice, remain poorly understood. Based on carbon and water vapor flux data obtained by the eddy covariance technique in a subtropical hilly tea plantation in southeast China during 2014–2018, this study analyzed the seasonal variations in gross primary productivity (GPP), evapotranspiration (ET) and ecosystem WUE, and discussed the response of GPP, ET and WUE to environmental variables during different seasons. The results showed that the mean annual GPP, ET and WUE ranged from 1426.61 ~ 1896.05 g C m⁻², 607.05 ~ 805.83 mm and 2.22 ~ 2.68 g C kg⁻¹ H₂O, respectively. At the daily time scale, GPP and ET responded significantly and positively to variations in air temperature (Ta), water vapor pressure deficit (VPD), and net radiation (Rn) in both the pruning season and late growing season, but daily WUE had a significantly negative response to variations in Ta, VPD and Rn. Rn was identified as the dominant factor in regulating GPP and ET during both the pruning season and late growing season, while the dominant factor controlling daily variations in WUE was VPD during the pruning season and Ta during the late growing season. Such results were mainly due to the divergent responses of carbon assimilation and water loss to different environmental variations and management strategies. These findings highlighted the importance of understanding the coupled processes between carbon assimilation and water loss in tea plantations.