A calibration apparatus includes a processor, an alignment device, and an arm. The alignment device captures images in a three-dimensional space, and a tool is arranged on a flange of the arm. The processor records a first matrix of transformation between an end-effector coordinate-system and a robot coordinate-system, and performs a tool calibration procedure according to the images captured by the alignment device for obtaining a second matrix of transformation between a tool coordinate-system and the end-effector coordinate-system. The processor calculates relative position of a tool center point of the tool in the robot coordinate-system based on the first and second matrixes, and controls the TCP to move in the three-dimensional space for performing a positioning procedure so as to regard points in an alignment device coordinate-system as points of the TCP, and calculates the relative positions of points in the alignment device coordinate-system and in the robot coordinate-system.