Qinghai spruce (Picea crassifolia) is the dominant species in the forest ecosystem of Qilian Mountains and is critical to the eco-hydrological processes of the ecosystem. Canopy coverage of Qinghai spruce is an important indicator of ecosystem quality, but there has been a lack of effective methods for its estimation. Hemispherical photography has shown great potential for the estimation, while little is known about the effect of weather conditions on this method. This study estimates canopy coverage of Qinghai spruce in Pailugou watershed of Qilian Mountains using hemispherical photography. Specifically, the effect of weather conditions, such as cloudy vs. clear days, on the estimation of the threshold values is evaluated. The estimation is compared with that of a traditional method. Results show that weather conditions have noticeable effects on the threshold estimation. The average threshold values are 118 and 149 for the cloudy days and clear days, respectively. When comparing between the hemispherical photography and the traditional method, the maximum difference between the estimations is 17.88% and minimum is 5.34%. In sum, this study demonstrates a promising method for the estimation of canopy characteristics of forest ecosystem that are valuable parameters for eco-hydrological modeling.