We analyze the effects of roughness in the magnitude of the magnetic field produced by a current carrying microwire, which is caused by geometric fluctuation of the edge of wire. The relation between the fluctuation of the trapping potential and the height that atom trap lies above the wire is consistent with the experimental data very well, when the colored noise with a finite correlation length is considered. On this basis, we generate the random potential and get the density distribution of the BEC atoms by solving the Gross-Pitaevskii equation, which coincides well with the experimental image, especially in the number of fragmentations. The results help us further understand the nature of the fluctuation and predict the possible application in the precise measurement.