A mechanical arm calibration system and a mechanical arm calibration method are provided. The method includes: locating a position of an end point of a mechanical arm in a three-dimensional space to calculate an actual motion trajectory of the end point when the mechanical arm is operating; retrieving link parameters of the mechanical arm, randomly generating sets of particles including compensation amounts for the link parameters through particle swarm optimization (PSO), importing the compensation amounts of each of the sets of particles into forward kinematics after addition of the corresponding link parameters, to calculate an adaptive motion trajectory of the end point; calculating position errors between the adaptive motion trajectory and the actual motion trajectory of each of the sets of particles for a fitness value of the PSO to estimate a group best position; and updating the link parameters by the compensation amounts corresponding to the group best position.