To comprehend the water purification process of Water Source Heat Pump (WSHP) water treatment system and improve the efficiency of WSHP, the fluorescence of DOM in water treatment system was studied with three-dimensional fluorescence spectroscopy. The results showed that the WSHP water treatment system has poor effect on the treatment of DOM, which has long been neglected, which affecting energy efficiency of WSHP. The filter cleaning cycle has a significant effect on the removal of protein organic components, microbial metabolites and humus. The HIX index of water in the system smaller than 4, and the main source of DOM is microbial metabolites. A long cleaning cycle will cause the system internal sludge clogging, triggering the DOM leak. The rich fulvic acid and protein organic components may be derived from Cyclotella sp., and humus may be derived from other algae. DOM removal effect is mainly affected by the filter operating cycle. To prevent the scaling problem in WSHP, more water treatment measures, such as frequent cleaning and intensive processing, should be taken to enhance the efficacy of WSHP.