Valuable archives of paleoenvironmental changes are scarce in the hinterlands of deserts. Calcareous root tubes (CRTs), a form of pedogenic carbonate, are widely distributed in the hinterland of the Tengger Desert, Northwest China. The investigations of delta C-13 and delta O-18 values within CRTs from the Tengger Desert have a great potential to provide new significant archives for paleoenvironmental reconstructions in this area. In this study, 30 CRT samples from the Tengger Desert were collected. All the samples were described using cathodoluminescence (CL), and their delta C-13 and delta O-18 values were measured. The results revealed that limited marine carbonate was incorporated in the CRTs in the Tengger Desert and delta C-13 and delta O-18 values of the inner belt of the CRTs were not affected by recrystallization. Therefore, delta C-13 and delta O-18 values of the CRTs could accurately record environmental conditions in the Tengger Desert. The carbon source of the CRTs was a mixture of soil CO2 derived from root respiration and atmospheric CO2. Furthermore, delta C-13 values of most samples were lower than - 3.0%, indicating that C-3 vegetation was the main vegetation in the Tengger Desert during the middle and late Holocene. Moreover, delta O-18 values of the CRTs were ultimately inherited from summer precipitation. Influenced by the 'amount effect' in summer and strong evaporation, the lower delta O-18 values of the CRTs revealed that relatively higher effective moisture occurred from 7 to 4 cal kyr BP while the higher delta O-18 values indicated that relatively lower effective moisture occurred from 4 to 2 cal kyr BP in the Tengger Desert. The Holocene millennial-scale moisture changes in the hinterland of the Tengger Desert suggest an arid early Holocene (11.7-7 cal kyr BP), a relatively humid mid-Holocene (7-4 cal kyr BP), and a humid to arid late Holocene (4-2 cal kyr BP). The discrepancy of effective moisture change reconstruction based on the CRTs in the Tengger Desert and adjacent lake sediments during the early Holocene demonstrated that the reliability of the reconstructed results from lake sediments during this period needs further investigation.