This paper presents a novel joint geometric camera calibration system using a novel calibration target for a visible and a far-infrared (FIR) cameras. By using the proposed calibration target which is the two-layer structure with different combinations of thermal emission, we can stably and precisely obtain the corresponding points of the checker pattern in the calibration target from the visible and the FIR images. The simple calibration algorithm based on the well-known Zhang's algorithm can accurately estimate the camera parameters, because we can use many useful tools which contribute the accuracy. Experimental results show that the proposed calibration system enables us to easily calibrate the visible and the FIR image with high accuracy compared with an existing system. Furthermore, the proposed system can lead to develop various applications including joint image denoising, and joint image up-sampling.