In order to improve the precision of simulated supercontinuum (SC) generation, the split-step Fourier algorithm is modified without increasing the computation amount. Traditional algorithm only refers to the dispersion coefficient of the central frequency. Due to the wide range of the supercontinuum, the error of the result would be big by using the traditional algorithm if the slope of the dispersion coefficient is large. According to the modified algorithm, the pulse could be regarded as the combination of many elements each with only one frequency. The elements with different frequencies could be processed seperately by using the modified algorithm, so the dispersion coefficients of all the frequencies could be refered to. The modified algorithm is applied in simulating the supercontinuum generation in the photonic crystal fibers with one and two zero dispersion wavelengths. And the results are compared with those of traditional algorithm. The simulation results show that the superiority of the modified split-step Fourier algorithm is not obvious in the photonic crystal fibers (PCF) with only one zero dispersion wavelength, but having certain superiorities in simulating the supercontinuum generation of the photonic crystal fibers with two zero dispersion wavelengths.