Through organic matter analysis of about 118 samples of sediment from the Dianchi Lake, it was found out that the content of organic matter ranged from 40.00g/kg to 90.00g/kg. Based the charts of 0~5cm, 5~10cm and 10~20cm sediment layers with GIS, it could be inferred that the organic matter content of Caohai was evidently higher than that in Waihai; the organic matter content of Waihai declined with the depth. A further explanation will be explored of the relationship between organic matter content and environment. The findings of the research will serve as basic reference for pollution control in the Dianchi Lake.