The invention relates to a method and a system for acquiring the three-dimensional coordinates of unknown points on the tower top of a high tower, and relates to the field of engineering measurement.The method comprises the following steps: measuring the three-dimensional coordinates of phase control points positioned on the tower top of the high tower; obliquely shooting the tower top, and carrying out digital marking on a picture with the phase control points in the shot picture, wherein the digital marking is used for marking the phase control points on the picture; transmitting the three-dimensional coordinates of all phase control points and all shot photos to a cloud computing platform; and generating a local real-scene three-dimensional model on the tower top of the high tower according to all shot photos and the three-dimensional coordinates of all phase control points by the cloud computing platform, wherein the local real-scene three-dimensional model has the three-dimensional coordinates of all position points, and a measuring person can obtain the three-dimensional coordinates of any point through a mobile terminal. According to the method, a plurality of groups of personnel and instrument operations are input in the high tower construction measurement, and the problem that a total station is difficult to observe the sighting conditions of the tower top of the hightower from the ground is solved.