For utilizing phosphogypsum effectively in cement, by measurement techniques such as infrared spectrum and color mass spectrum et al, organic matters in phosphogypsum were analyzed qualitatively and quantitatively. Their influence on the properties of cement was also investigated. The results showed that organic matters in phosphogypsum were mainly C5H10O3, C2H3O5, C6H14O, C5H10O2. They were physically adsorbed on the surface of phosphogypsum crystals and their content fell within the range of about 0.1%~0.2%. The presence of organic matters increased the setting time of cement and reduced the strength, particularly remarkablely in the 28 days compressive strength. Their influence could be cleaned out by floating pretreatment.