To address the challenges of water resource stress and ecological response in desert ecosystems of arid inland river basins under climate change, this study focuses on a typical desert ecosystem in the lower reaches of the Manas River Basin of the arid inland river in northwest China as the research object. Using the eddy correlation method, we simultaneously monitored the latent heat flux (LE), sensible heat flux (H), Bowen ratio (B), air temperature (TA), relative humidity (RH), saturated water vapor pressure (VPD), and average wind speed (WS) at the southern edge of the Gurbantunggut Desert. The Pearson correlation coefficient was applied to examine the characteristics of water and heat flux variations and their environmental impact factors in desert ecosystems from April to October 2023 and 2024. The main findings are summarized as follows. (1) At the half-hour scale, LE and H exhibited a unimodal pattern, with the maximum occurrence time of 13:00—15:00. The LE peak occurred 1-2 h earlier than that of H. The main environmental factors affecting LE were TA (r=0.63)>VPD (r=0.62)>WS (r=0.51), while those affecting H were WS (r=0.73)>VPD (r=0.61)>TA (r=0.56)>RH (r=-0.33). The main environmental factor affecting B was WS (r=0.11). (2) At the daily scale, H and LE exhibited clear seasonal variation characteristics, initially increasing and then decreasing, forming a “U” shaped trend, and B gradually flattened in the middle of growth. TA and VPD were the main environmental factors affecting LE wheile WS and RH mainly affected H. (3) At the monthly scale, the change in water heat flux showed a similar trend, with H and LE showing unimodal variations. LE was highest in July and August and lowest in October. H peaked in June and July and also reached its minimum in October. LE showed strong positive correlations with TA, VPD, and RH, with TA having the strongest positive correlation (r=0.85). H was mainly influenced by TA, VPD, and WS, with TA and VPD showing strong positive correlations (r=0.85 and 0.83, respectively). The main environmental factors affecting B were WS, TA, VPD, and RH, with RH showing a negative correlation. This study provides insights into the variation patterns of water and heat flux and their relationships with environmental factors across multiple time scales in the desert ecosystems of arid inland river basins, offering a theoretical foundation for the ecological construction of desert ecosystems.