Photonic crystal fibers have been widely used in the supercontinuum generation of femtosecond pulse laser sources. When the repetition rate of a laser source is low, the evolution of supercontinuum over time is slow, which is usually not noticed. In applications such as calibrations of astronomical spectrometers, high repetition rate laser sources of the order of gigahertz to tens of gigahertz are required. In this case, the supercontinuum degradation is significant within a limited time period. Using 1040nm femtosecond laser as the pump source, by testing the evolutions of supercontinua of three photonic crystal fibers with different air-filling fractions, it is found that the degradation process accelerates with the increase of the air-filling fraction. Accompanying the degradation of supercontinuum, multiple bright spots of different colors appear in the section where the supercontinuum is generated on the fiber. It implies a directional light leakage phenomenon. Observing the spectral absorption of the spectrally degraded fiber confirmed that the main reason for the degradation is not the generation of massive non-bridged oxygen color centers in the fused silica material. Based on the directional characteristic of the light leakage, a theory that a long-period grating formation in the fiber core by multiphoton absorption is proposed. In order to search for the factors that affect the supercontinuum generations of the photonic crystal fibers, so that the goal of suppressing the degradation can be achieved, firstly, parameters of the fiber tapering are changed. It is expected that the photon tolerance of the fused silica material of the fibers can be enhanced. The experimental results show that the effectiveness is scant. Then, experiments are carried out with maintaining the average power of the laser source, reducing the peak power of the laser pulse and maintaining the peak power of the laser pulse, reducing the average power of the laser source. It is shown that the total amount of high peak power pulses coupled into the optical fiber in a certain time period is the most important factor affecting the supercontinuum degradation. In the application of astronomical spectrometer calibration, the demand for optical power of supercontinuum is not high. Using a chopper to reduce the average power of the incident light of the photonic crystal fiber is an effective, simple and feasible method to slow down the supercontinuum degradation.