A progressive warming or a long-term cooling trend during the Holocene remain controversial both at a regional and global scale. One possible reason for this discrepancy could be seasonality and uncertainties in the biases of various temperature proxies. Here, we present the distributions of archaeal isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) from two soil transects in Arid Central Asia (ACA): a temperature (elevation) transect at Mount (Mt.) Tienshan (n = 18) in Northwest China and a precipitation transect in northern Iran (n = 48), to assess the impacts of temperature and precipitation on the distributions of soil iGDGTs, respectively. In addition, changes in archaeal community structure are detected by high-throughput sequencing in 9 soils from different elevations at Mt. Tienshan. Thereafter, a well-constrained, soil iGDGT-based Holocene temperature reconstruction is obtained for the first time from a loess-paleosol sequence (LJW10) at Mt. Tienshan. Our results indicate that mean annual air temperature (MAAT) dominates the distribution of soil iGDGTs, and the TEX₈₆ (TetraEther indeX of tetraethers consisting of 86 carbon atoms) proxy exhibits significant positive correlations with MAAT in ACA. There is no direct evidence that seasonal changes in temperature and non-thermal factors (e.g., MAP) significantly influence soil TEX₈₆ in ACA, which is further supported by a dominance of Thaumarchaeotal Group I.1b in Mt. Tienshan soils. Based on the local soil TEX₈₆-MAAT calibration from Mt. Tienshan, the estimated MAAT value of the topmost sample from the LJW10 section agrees well with the instrumental MAAT. Our MAAT record supports the long-term warming trend observed in numerous Northern Hemisphere (NH) annual/winter temperature records, model simulations and paleoclimate data assimilation, which may be primarily attributed to the changes in annual mean insolation, greenhouse gases and NH ice sheets dynamics.