Canopy water use efficiency (cWUE) and ecosystem water use efficiency (eWUE) provide critical insights into analyzing plant water-use strategies and the carbon-water coupling patterns in agroecosystems. This study analyzed four consecutive years of flux data, including gross primary productivity (GPP), net ecosystem productivity (NEP), evapotranspiration (ET), and transpiration (T), from a subtropical drip-irrigated citrus orchard in Southwest China, to quantify seasonal variations in eWUE and cWUE and identify their environmental controls during the growing and non-growing seasons. Results showed that eWUE exhibited pronounced seasonal dynamics, peaking in winter (non-growing season), declining to a minimum during summer (peak GPP and ET period). Consequently, mean eWUE was significantly higher in the non-growing season (5.39 g C kg⁻¹ H₂O) than that of the growing season (3.64 g C kg⁻¹ H₂O, p < 0.05). In contrast, cWUE showed relatively stable seasonal dynamics, with statistical values of 2.49 g C kg ⁻¹ H₂O in the growing season and 2.81 g C kg ⁻¹ H₂O in the non-growing season, respectively. During the citrus non-growing season, cumulative GPP, NEP, ET, and T accounted for 21%, 24%, 16%, and 24% of their respective annual totals, the corresponding portions during the growing season were 79%, 76%, 84%, and 76%, respectively. The structural equation model revealed that ET drove eWUE variations interannually, while cWUE was mainly regulated by NEP during the growing season and by T during the non-growing season. These findings underscore the important contribution of non-growing season carbon and water fluxes to the annual carbon-water balance, and reveal that scale-dependent carbon-water processes and redefine the carbon sink potential of a typical citrus ecosystem in Southwest China.