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Canopy conductance (Gc) largely regulates carbon/water cycling and land–atmosphere interactions, but quantifying Gc using eddy flux data is limited by the difficulty of partitioning plant transpiration (T) and surface evaporation (E). We introduced an underlying water use efficiency (uWUE) method to partition evapotranspiration (ET) in an oasis maize ecosystem, and cross–compared with the Shuttleworth and Wallace (SW) model, the lysimeter and isotope measurements. We then estimated surface conductance (Gs) by ET and Gc by T partitioned using the uWUE method, followed by a performance evaluation on the Jarvis model parameterized with both Gs and Gc. The results showed that T/ET estimated by the uWUE method was close to the isotope method in the peak growing season of 2012, it showed similar seasonal variations with the lysimeter/eddy covariance method and the SW model throughout this growing season. Daily T partitioned by the uWUE method was in good agreement with the SW model from 2012 to 2015 (r2 = 0.91). Additionally, Gc had more significant seasonal variations than Gs. The Jarvis model parameterized with Gc exhibited superior performance than those with Gs. Our study suggests that the uWUE method can exclude influences of nonstomatal conductances, and will have great potential to provide more reasonable parameterization for simulation of plant stomata.