A method and system for measuring three-dimensional coordinates of an object are provided. The method includes: capturing images from a calibration point of known three-dimensional coordinates by two image-capturing devices disposed in a non-parallel manner, so as for a processing module connected to the image-capturing devices to calculate a beam confluence collinear function of the image-capturing devices; calibrating the image-capturing devices to calculate intrinsic parameters and extrinsic parameters of the image-capturing devices and calculate the beam confluence collinear function corresponding to the image-capturing devices; and capturing images from a target object by the image-capturing devices so as for the processing module to calculate three-dimensional coordinates of the object according to the beam confluence collinear function. In so doing, the method and system enable the three-dimensional coordinates and bearings of a target object to be calculated quickly, precisely, and conveniently. Hence, the method and system are applicable to various operating environments.