Quantitative assessment of water-heat exchanges between forests and grasslands and the atmosphere in the Qilian Mountains contributes to a deeper understanding of the water cycle and energy balance processes in vegetated ecosystems. In this study, half-hourly and daily water heat flux data of forests and grasslands on the northern slopes of the Qilian Mountains in 2023 were obtained based on eddy covariance techniques, and the daily and seasonal characteristics of latent heat flux (LE), sensible heat fluxe (H), and Bowen ratio (β) of forests and grasslands were compared and analyzed, Structural equation modeling (SEM) and Pearson correlation analysis (Pearson) were used to explore the effects of eight environmental factors, namely, net radiation (Rn), air temperature (Ta), wind speed (u), rainfall (P), saturated vapor pressure difference (VPD), relative humidity (RH), soil temperature (Ts), and volumetric soil water content (VWC), on the water-heat flux. The results of the study showed that (1) the daily changes of LE and H in forest and grassland showed a single-peak pattern, with the daily mean value of LE in forest higher than that in grassland, and the daily mean value of H in grassland higher than that in forest; (2) The seasonal changes of forest and grassland LE are single-peaked, the seasonal changes of H are bimodal, and the seasonal changes of β are U-shaped; the monthly mean value of forest LE is higher than that of grassland, the monthly mean values of grassland H and β are higher than that of forest, and the value of β is greater than 1 in summer, and the value of β is less than 1 in the rest of the seasons, and summer Heat exchange between the earth and air was dominated by latent heat form, and the rest of the season was dominated by sensible heat form; (3) Eight environmental factors were correlated with forest and grassland LE, H, and β in the growing season, and P and SWC were not correlated with forest and grassland LE, H, and β in the non-growing season, and the degree of correlation was stronger in the growing season than in the non-growing season, and the degree of correlation in the grassland was stronger than in the forest. Throughout the year, LE, H, and β are mainly affected by the direct positive influence of Rn, u, and VPD, and the direct negative influence of RH, in addition, Rn indirectly affects LE, H, and β by affecting u, VPD, and RH, and VPD indirectly affects LE, H, and β by affecting RH and u. The results of this study can provide a theoretical basis for the management and effective utilization of forest and grassland water resources on the northern slopes of the Qilian Mountains.