The invention discloses a method for controlling the precision of a drilling trajectory. The method includes the following steps that a predetermined trajectory of a drill rod is determined; a main shaft of the drill rod is divided into finite elements, and the parameter, element mass (please see the description), total weight M and rigidity K of the rill rod are obtained; According to the formula (shown in the description), drill rod offset control is conducted, the allowable offset Ep is set, the rotating speed Omega of the drill rod can be obtained through MATLAB software, in the drilling process, by controlling the drilling speed, the water supply amount of a main pump is reduced, the pressure of water in a hole is reduced, and the actual drilling trajectory is controlled. When the method is applied to control over precision of guide hole digging trajectory of raise-boring machine, related parameters are obtained, a drilling scheme is formulated, after offset occurs, according to the requirement of the scheme, the drilling speed is increased, the method is cooperated with the GPS in use, by controlling the rotation speed and the drilling angle of the drill rod in the inclined shaft excavation process, the drilling depth is positioned in the construction process, and the inclined shaft construction with the guide hole trajectory precision controlled can be achieved.