Disclosed herein are workstation, medical imaging apparatus having the same and method for controlling thereof. The medical imaging apparatus includes an X-ray source configured to irradiate X-rays; an X-ray detector configured to obtain raw data by detecting X-rays irradiated from the X-ray source; and an image processor configured to determine a motion parameter to represent motion of at least one of an object, the X-ray source, and the X-ray detector from a medical image reconstructed based on the obtained raw data, and reconstruct a motion-compensated medical image of the object based on a virtual trajectory of the X-ray source generated based on the determined motion parameter.