In this paper, we present a novel low-loss splice for use between the photonic bandgap fiber (PBGF) and the conventional step index fiber to make PBGFs more functional. The gap between the butt-coupled fibers is the most important parameter for maintaining good output coupling efficiency and allowing gas diffusion. To achieve the small gap, a focused ion beam (FIB) milling technique was developed to clean the fiber surface. The gap is adjustable from 0 to 400 µm, and the typical connection loss at a gap of 20 µm is 1.6 dB. A measurement system for low gas concentrations based on the PBGF cell has been developed and implemented. Experiments for measuring ammonia gas at the ppm level were performed. The basic peak agreed well with the database of the Pacific Northwest National Laboratory (PNNL), meaning that this method can be used to accurately and effectively measure gas concentration.