The canopy transpiration of forests is one of the most important components in the water balance and it is nevertheless the least-understood component primarily because systematic data from field environment are unavailable and difficult measure. Modeling thus remains to be an effective tool in estimating the canopy transpiration of forests. Qinghai spruce (Picea crassifolia) forest plays an important role in regulating the water balance in the Qilian Mountains through its effects on different hydrological components (including rainfall interception, canopy transpiration, and soil infiltration) and again the canopy transpiration of the forest is the least-understood component. This study aimed at estimating the canopy transpiration of Qinghai spruce forest of the Qilian Mountains based on the meteorological and the energy influx data observed at Guantan Forest Station (100°15'0.8″ E,38°32'1.3″ N) within the Qilian Mountains. Specifically, this study simulated the canopy transpiration of the Qinghai spruce forest during the growing season of 2008 using an improved Penman-Monteith equation and the univariate sensitivity analysis was performed to test the sensitivity of variables affecting the canopy transpiration. The results indicate that the total transpiration of Qinghai spruce forest in the growing season (from May to September) of 2008 is 148.8 mm and the daily canopy transpiration rate ranges between 0.016 and 2.19 mm with a mean daily transpiration rate is 0.97 mm at the research station. The highest monthly canopy transpiration occurs in June (37.9 mm) and the lowest in September (17.3 mm). The modeled daily canopy transpiration increased at the beginning of May and reached minimal value towards end of the growing season. It is noticeable that the daily canopy transpiration reached its maximum in the middle of July, but the maximal monthly transpiration occurred in June probably because of more rainy and cloudy days in July that effectively lowered both air temperature and solar radiation, thus lowering the monthly canopy transpiration. Sensitivity analysis showed that among the factors affecting the canopy transpiration, the sequential order of the importance is as follows: net radiation intercepted by canopy > leaf area index > daily air temperature > wind speed > relative humidity. Apparently, the net radiation intercepted by canopy and the leaf area index are two most crucial factors and thus the accuracy of the simulated results are dictated by the accuracies of these two parameters. The instrumental error of measuring the net radiation was ±10% in the study. The leaf area index was obtained from digital hemispherical photograph that demonstrated the best way to get the leaf area index in the forest. Our sensitivity analysis showed that ±10% changes in the net radiation resulted in a maximal change of ±0.22 mm (±10%) in the daily canopy transpiration rate. The ±10% changes in the estimated leaf area index can result in a maximal change of 0.16 mm (+7.22%) or -0.15 mm (-6.90%) in the daily canopy transpiration rate. We consider that less than ±10% change in the estimated daily canopy transpiration resulted from about ±10% change in any of the contributing factors and thus the model-based estimation of the daily canopy transpiration is acceptable.