Polycyclic aromatic hydrocarbons as a universal concern in the monitoring of priority pollutants have low content in the water environment and are interfered with the coexistence of humic acid. The spectra of humic acid and polycyclic aromatic hydrocarbons overlap seriously, so it was difficult to use the conventional methods for rapid quantitative detection. As a model compound of polycyclic aromatic hydrocarbons, Phenanthrene (PHE) was chosen in the experiment. The fluorescence spectra of PHE and humic acid (HA) were investigated by three dimensional fluorescence excitation-emission matrix. The method combined excitation-emission matrix fluorescence spectra with parallel factor analysis and was applied to determine PHE and HA directly. The excitation wavelength changed from 240 to 360 nm at an interval of 5 nm. The emission wavelength varied from 260 to 575 nm at an interval of 5nm. The satisfactory results show that this experiment can be easily performed without paying out time-consuming and complicated procedures.