The invention relates to the technical field of perpendicularity measurement, and discloses a method for measuring the perpendicularity of a tower crane attached to a seismic isolation structure. Themethod comprises the following steps of, S1, after the tower crane is attached to an overground structure, starting detection, setting a reference point at a measurement point, setting a rear view point in the vicinity of the reference point, pasting a reflection sheet at the tower body part, and recording initial coordinates for later positioning measurement of a total station; S2, erecting the total station at the reference point for recording coordinates, and rechecking whether the reference point is accurate or not through a prism at the rear viewpoint; S3, measuring the reflection sheet of a tower body through the total station and feeding back coordinate information; and S4, judging that the tower body of the tower crane is tilt through periodic tower body coordinate analysis if beyond the allowable deviation range, and avoiding similar phenomenon by taking effective measures. According to the method for measuring the perpendicularity of the tower crane attached to the seismic isolation structure, accurate measurement can be performed through use of the total station and control of the coordinates of reflection points of the tower body, the measurement is more accurate than that of a traditional theodolite, and the measurement result and the basis are more full.