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Estimation of vegetation chlorophyll content is crucial for understanding carbon balance and for assessing stress and vulnerability of desert ecosystems. This study evaluated LIBERTY and PROSPECT, both the radiative transfer models at leaf scale, for estimating the chlorophyll content of Haloxylon ammodendron assimilating branches inversely from measured reflectance spectra. The results showed that both original LIBERTY and PROSPECT exhibited tangible challenges for inversion using measured data. However, their calibrated versions were capable of accurate retrieval of chlorophyll content inversely from reflectance spectra. For calibrated LIBERTY, the inversed estimation recorded an R 2 of 0.55 with an RMSE of 34.33 mg m2 over the entire measured chlorophyll range from 47.03 to 291.83 mg m2. For comparison, the R 2 reached 0.53 with an RMSE of 34.76 mg m2 for the calibrated PROSPECT. Further validations with other independent data sets produced similar high chlorophyll estimation accuracies. Our results indicated that both LIBERTY and PROSPECT are applicable for estimating chlorophyll content inversely for assimilating branches of typical desert plants after careful calibration, which is a necessary prior when coupling with canopy models to make further stand level chlorophyll estimations.