The chirp effect in supercontinuum (SC) generation in photonic crystal fibers (PCFs) is researched carefully in experiment. Using an acoustic-optics programmable dispersive filter (AOPDF), the 1-4 order dispersions of the pulses from femtosecond oscillator can be accurately controlled. The experimental results show the SC generation in PCF is sensitive to the chirp of incident pulse, and the output spectrum and conversion efficiency can be tuned by changing the initial dispersion state. With different group delay dispersion (GDD) brought to the incident pulse, we find that positive chirp can enhance the energy conversion to long wavelength, and negative chirp can enhance the conversion to short wavelength. Specially, an optimal negative chirp can maximize the conversion to the shortest one at about 625 nm. The effect of the third-order dispersion (TOD) also has been investigated, and we find that the same value of the positive and negative TOD has the similar effect on the SC.