The invention discloses a high-precision drilling method of a small drilling machine. The method comprises the following steps that a drilling system is moved to be close to the surface of a workpiecethrough a three-stage tool setting device, the workpiece is moved through cooperation of a first-stage tool setting device and a second-stage tool setting device, and finally positioning alignment iscompleted between a workpiece drilling point and the drilling system; a worker directly pulls the drilling system to descend through the three-stage tool setting device and drills a through hole in the workpiece; the worker makes the drilling system to be in contact with a drilling point on the surface of the workpiece through the three-stage tool setting device; the worker adjusts a coarse adjustment component and a fine adjustment component, so that the drilling device descends along with the coarse adjustment component and the fine adjustment component, the workpiece is subjected to high-precision non-through hole drilling, and meanwhile the worker can read the drilled hole depth in real time according to a display component.