A far-infrared (FIR) image contains important invisible information for various applications such as night vision and fire detection, while a visible image includes colors and textures in a scene. We present a coaxial visible and FIR camera system accompanied to obtain the complementary information of both images simultaneously. The proposed camera system is composed of three parts: a visible camera, a FIR camera, and a beam-splitter made from silicon. The FIR radiation from the scene is reflected at the beam-splitter, while the visible radiation is transmitted through this beam-splitter. Even if we use this coaxial visible and FIR camera system, the alignment between the visible and FIR images are not perfect. Therefore, we also present the joint calibration method which can simultaneously estimate accurate geometric parameters of both cameras, i.e. the intrinsic parameters of both cameras and the extrinsic parameters between both cameras. In the proposed calibration method, we use a novel calibration target which has a two-layer structure where thermal emission property of each layer is different. By using the proposed calibration target, we can stably and precisely obtain the corresponding points of the checker pattern in the calibration target from both the visible and the FIR images. Widely used calibration tools can accurately estimate both camera parameters. We can obtain aligned visible and FIR images by the coaxial camera system with precise calibration using two-layer calibration target. Experimental results demonstrate that the proposed camera system is useful for various applications such as image fusion, image denoising, and image up-sampling.