Subalpine forest ecosystems are crucial in the global carbon dioxide (CO2) and water (H2O) cycles. Based on the observation data of a Qinghai spruce forest ecosystem in the Qilian Mountains in northwestern China, we quantified the extents of CO2 and H2O fluxes, represented by net ecosystem CO2 exchange (NEE), gross primary production (GPP), and ecosystem respiration (Re) for the former and evapotranspiration (ET) for the latter, and calculated the ecosystem water use efficiency (WUEe). Then, we investigated the key controlling factors for NEE, GPP, Re, and ET. The results revealed obvious seasonal fluctuations in NEE, GPP, Re, and ET, with greater absolute values during the main growing periods of Qinghai spruce (April to September) from 2018 to 2020. The Qinghai spruce forest ecosystem was always a robust carbon sink, and the ET values were quite close to the amount of precipitation (P), indicating that most of the water resources supplied by P are consumed by the ET. The WUEe values were higher than that of similar ecosystems. NEE and GPP were mainly dominated by the net radiation (Rn) and soil temperature (Ts). For ET, it was mainly controlled by Rn, Ts, vapor pressure deficit (VPD), and relative humidity (RH). The capacity of carbon sinks in the Qinghai spruce forest ecosystem may be reduced by global warming, which could also promote ET and cause drought stress, further decreasing the carbon sequestration of the forest. This study would provide direction for the ecological restoration of the Qilian Mountains in the future.