This article introduces the general situation of Wenchuan earthquake scientific drilling project and the progress of drilling and logging engineering of the project. The characteristics of earthquake scientific drilling are analyzed and the organizational management for the implementation of the holes WFSD-1, WFSD-2 and WFSD-3-P is summarized. On the basis of organization and management experiences of Chinese Continental Scientific Drilling Project, the improvement measures on the organizational management for the Wenchuan project were discussed and put forward on the consideration of the exploration, complicated formations and engineering plan with frequent changes to meet the requirement of geoscientific research.