A three-dimensional printing apparatus and a method for calibrating printing inaccuracy thereof are provided. A printing head of the three-dimensional printing apparatus is adapted for moving along a straight printing path on a datum plane and simultaneously feeding out forming material, so as to generate a layer object on a supporting surface of a platform. If a path distance of the straight printing path is greater than a threshold, a plurality of linear compensation relationships respectively corresponding to a plurality of first zones of the supporting surface are used for calculating a first compensation value of a starting point and a second compensation value of an ending point. If the path distance of the straight printing path is not greater than the threshold, a common compensation values is decided based on at least one of second zones and which is corresponding to the starting point and the ending point.