In this paper, we propose a hybrid stereoscopic camera system which acquires and utilizes stereoscopic images from two different camera modules, the main-camera module and the sub-camera module. Hybrid stereoscopic camera can effectively reduce the price and the size of a stereoscopic camera by using a relatively small and cheap sub-camera module such as a mobile phone camera. Images from the two different camera modules are very different from each other in aspects of color, angle of view, scale, resolution and so on. The proposed system performs an efficient hybrid stereoscopic image registration algorithm that transforms hybrid stereoscopic images into normal stereoscopic images based-on camera geometry. As experimental results, the registered stereoscopic images and applications of the proposed system are shown to demonstrate the performance and the functionality of the proposed camera system.