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We present a self-consistent charge density functional tight-binding (SCC-DFTB) parameterization for boron clusters. In the parameterization we devote more attention to the repulsive energy in the SCC-DFTB theory and examine the quality of the parameter fitted to different sets of reference structures. To test the quality of the parameter, we combine the SCC-DFTB with modified basin hopping method (MBH) to search for global minima of small boron clusters Bn (n=3-13). In closer examinations, we found the repulsive potential fitted to trimer is a compromise among the reference structures judging from the variation of the potential curve and the geometry that it yields. On comparing further our calculated lowest energy boron clusters are very good agreement with other theoretical calculations.