Three-dimensional light field imaging in laparoscopic surgery is an emerging technology, which has the potential to enable three-dimensional imaging. Calibration of the three-dimensional light field endoscope (3D LFE) is essential but challenging as the disparity is much smaller than that of the conventional light field camera. The geometrical model for 3D LFE is established, and a calibration method based on virtual objective lens and virtual feature points is proposed. First, the virtual objective lens is introduced and the parameters about it are calibrated using corner features in center subaperture images. Second, two types of virtual feature points are proposed to calibrate the parameters about the microlens array, one is on the black-and-white board line and the other is selectively determined but can be anywhere on the checkerboard. Moreover, the relationship between the virtual feature points mapping in the microlens image and the virtual feature points mapping in the central subaperture image is deduced to overcome tiny light field disparity. Experimental results verify the performance of our calibration method.