Five healthy Haloxylon ammodendron trees were randomly selected to monitor the photochemical reflectance index (PRI) and its relation to light use efficiency (LUE) in shaded and sunlit assimilating branches. Linear regression was performed where the results revealed that LUE decreased with seasonal courses with vivid midday depression regardless of light variation within canopies. PRI and LUE decoupled in early spring when the foliage was deeply downregulated, with high correlation (, ) during most parts of the year. Measured and estimated LUE were highly correlated for the July to September dataset (, ) compared to May to June datasets (, ). The estimated LUE for young assimilating branches could be obtained with a high RMSE of 0.01, compared to mature branches with an RMSE of 0.003. The measured LUE values were higher than estimated LUE during the period from May to June, and values were slightly lower at the end of the growing season. This was attributed to differences in the physiological and biochemical mechanisms controlling the seasonal dynamics of PRI. Therefore, PRI is the best estimator of LUE when age-related changes and canopy light partitioning are considered in assimilating organs. Combined use of PRI with pigments could improve the remote evaluation of LUE.