Three-dimensional fluorescence spectra of polycyclic aromatic hydrocarbons (PAHs) in soil are directly recorded using a fluorescence spectrophotometer. To identify the components of PAHs in soil, nonsmooth non-negative matrix factorization (nsNMF) are used. Results show that NMF can effectively extract the fluorescence spectrum signal of a single PAH from the mixture spectrum. The similarity coefficient between the analytical spectra and corresponding reference spectra obtained by nsNMF under random initial values is all above 0.824, which is higher than that of the standard NMF based on alternating non-negative least squares (NMF/ANLS). In farmland soil, the similarity coefficients of phenanthrene and anthracene between the analytical spectra and corresponding reference spectra increased from 0.758 and 0.845 (NMF/ANLS) to 0.907 and 0.913 (nsNMF), respectively. The combination of three-dimensional fluorescence spectra and nsNMF can facilitate rapid identification of components of PAHs in soil.