Photonic crystal fiber can generate particular dispersion properties and highly nonlinear, because of the special guiding mechanism and the adjustable structure parameters, which provides new conditions for the study of nonlinear fiber optics. There are rich nonlinear spectral properties produced by a variety of nonlinear physical effect, under different pump light pulse parameters in photonic crystal fibers with different structure and transmission properties. At present many papers have reported the experimental results of nonlinear optical properties in photonic crystal fiber, but there is little theoretical analysis about the produced mechanism and the change rule of the nonlinear spectrum. In the paper, solving nonlinear Schrodinger equation with split-step Fourier method, transmission process of femtosecond laser pulse in photonic crystal fiber is simulated. The relationship between the output spectrum and incident light pulse parameters (the peak power of pump light P, the wavelength of pump light λ, the shape of light pulse, the width of light pulse TFWHM), the structure parameters of optical fiber (the pitch Λ, the hole-to-pitch ratio d/Λ, the length of fiber), the transmission characteristics (the dispersion properties, the nonlinear coefficient) is obtained. The spectral characteristics produced by nonlinear effects of the Raman soliton, dispersive wave, self-phase modulation are analyzed. The nonlinear optical spectrum of cladding note in photonic crystal fiber is studied in experiments, the broadband spectrum of soliton wave and dispersive wave is obtained. There are blue-shift dispersive wave near the wavelength of 0.5 μm, residual pump light near the wavelength of 0.82 μm, soliton wave near the wavelength of 1.1 μm, red-shift broadband dispersion wave near the wavelength of 2 μm in the spectrum obtained both in theory and experiment. The numerical simulation is confirmed through experimental observation. The physics principle of the nonlinear spectrum in photonic crystal fiber is revealed. These are useful and practical to realize the controllable output of broadband spectrum. These provide guidance for the structure design, fabrication, applied research of high nonlinear photonic crystal fiber.