After briefly introducing the management of Wenchuan earthquake scientific drilling project, including organization structure and management mode of the project, this article focuses on describing organization and management of drilling engineering of the project. In a six year period, five holes were drilled along Longmenshan earthquake fault zone. The drilling contract mode of the project changed from general contracting system to daily cost system. And incentive mechanism was introduced into daily cost system later. The article summarizes successful on-site experiences of drilling engineering management of the project and discusses management mode of scientific drilling projects, especially for those, whose formation and drilling conditions are very complicated. The experiences and understandings gained in this project will be useful for similar scientific drilling projects.