Some embodiments of the disclosure provide a method for measuring orthogonality of an orthogonal axis system, In some examples, the method includes following steps: placing an instrument on a bearing surface, intercepting a second rotary axis along an interception plane to obtain a first virtual cross section of the second rotary axis, and measuring the first virtual cross section to obtain a geometric center of the first virtual cross section as a first position; rotating a first rotary device to enable the second rotary axis to rotate with a preset angular degree, and measuring the second virtual cross section to obtain a geometric center of the second virtual cross section as a second position; and determining whether the orthogonality between the first rotary axis and the second rotary axis meets requirements or not on the basis of the first position and the second position.