The invention relates to a top drive type drilling machine system based on dynamic control of a tool surface of an underground drilling tool and a well drilling method. The drilling machine system comprises a dynamic control system and a well drilling system, wherein the dynamic control system comprises a dynamic measuring subsystem, a feedback control subsystem, a user interaction subsystem and an execution subsystem; a user inputs drilling tool information, well drilling fluid information, stratum information and a control strategy through the user interaction subsystem; a many-body dynamics model of a well drilling system is established by the feedback control subsystem according to the received drilling tool information, well drilling fluid information and stratum information; various information of the well drilling system in a well drilling process is measured by the dynamic measuring subsystem and is transferred to the feedback control subsystem; and the feedback control subsystem judges whether the tool surface of the underground drilling tool exceeds a set threshold value or not, calculates the required rotating angle of a top drive, the position of a traveling block and the pumping speed of a slurry pump in a many-body dynamics simulating manner, and drives the top drive, the traveling block and the slurry pump to run. The top drive type drilling machine system continues drilling until the tool surface of the underground drilling tool returns to a design position, and dynamic adjustment control on the tool surface of the underground drilling tool is finished.