In order to solve the problem that the traditional CNC systems and machine tool structures cannot be directly used in wood deep hole machining,the principle of deep hole machining was studied, and the important and difficult problems were analyzed. Research and elaboration were performed from several aspects: the special tooling fixture system and the main structure design of the machine tool, flexible auxiliary clamping system design of the machine tool, the electrical control system of the entire machine tool and PLC internal feed interpolation logic algorithms and so on. The pre-processed 16 mm hole was made by the wood deep hole drilling machine with an accuracy of 1599 mm, which can meet its processing requirements. The design and research of the wood deep hole drilling machine solves the problem of wood in automated deep hollow machining and provides a solution for the industry.