Method and navigation system for registering two-dimensional image data set with three-dimensional image data set of body of interest

A method for registering a two-dimensional image data set with a three-dimensional image data set of a body of interest is discloses herein. The method includes the following steps: adjusting a first virtual camera according to a distance parameter calculated corresponding to the two-dimensional image data set and the body of interest; rotating the first virtual camera according to an angle difference between a first vector and a second vector; and rotating the first virtual camera according to an angle which is corresponding to a maximum similarity value of a plurality of similarity values calculated in accordance with reconstructed images of the three-dimensional image data set which includes one generated by the first virtual camera and the others generated by other virtual cameras with different angles or different pixels from the one generated by the first virtual camera and the two-dimensional image data set.