Long scan time has hampered susceptibility weighted imaging (SWI) in routine clinical application to diagnose brain diseases related to venous vasculature. Compressed sensing (CS) was demonstrated to significantly reduce scan time of SWI by exploiting signal sparsity in wavelet domain. However the reconstruction time of CS based on wavelet sparsity is usually time consuming. In this study, the feasibility of applying CS in SWI with singular value decomposition (SVD)-based sparsity basis was investigated. It was found that CS reconstruction based on SVD sparsity basis can achieve reasonably high computing speed than that of wavelet-based sparsity basis, while still achieving accurate image reconstruction.