Abstract: The source and control mechanism of fusion splicing loss were analyzed for the splicing between the photonic crystal fibers with different air-hole fraction and single-mode fiber. The splice loss evolution with the splicing parameters, including the fusion current, fusion time, power of discharge, were experimentally studied. With a carefully adjustment, splicing loss as low as 0.22 dB was realized both for high and low air-hole fraction photonic crystal fibers. The fibers were used in experiments of generating supercontinuum and ytterbium doped large mode area photonic crystal fiber laser amplifier was used as pump source. Supercontinuum with power as high as 7.45 W and wavelength range from 650 nm to 1 750 nm was obtained.