The present invention relates to a system and a method for calibration between coordinate systems of a 3D camera and a medical imaging apparatus and an application thereof. The calibration system comprises: a calibration tool arranged on a scanning table, wherein the calibration tool is provided with markers and a reference point, the reference point is aligned with a center of the medical imaging apparatus to serve as an origin of the coordinate system of the medical imaging apparatus, and positions of the markers in the coordinate system of the medical imaging apparatus are calculated according to relative positions of the markers with respect to the reference point; a 3D camera for capturing images of the markers and determining positions of the markers in the coordinate system of the 3D camera based on the captured images; and a calculation device for calculating a calibration matrix using the positions of the markers in the coordinate system of the 3D camera and the positions of the markers in the coordinate system of the medical imaging apparatus, and performing calibration between the coordinate system of the 3D camera and the coordinate system of the medical imaging apparatus using the calibration matrix. The method corresponds to the aforementioned system. The present invention further relates to an application of the calibration and a computer-readable storage medium capable of implementing the method and the application.