Qizong hydropower station is a high dam and large reservoir built in the canyon area. The maximum dam height was preliminarily planned to be about 358m. The drilling sampling of deep overburden layer is essential means to find out its cause and engineering geological property, and also the important means for water resources and hydropower engineering geological investigation. Because of the thick coverage layer with bad homogeneity of component substances, drilling coring is difficult. The coring quality is directly related to the accuracy and detail of engineering geological investigation data. By the application of special drilling tools and SM plant gum drilling fluid, coring quality in deep overburden layer was improved. The paper discusses the drilling and coring process in the deep overburden layer by the engineering case of Qizong hydropower station.