The geostatistics method combined with geographic information system (GIS) was applied to the spatial variability of heavy metal in lake sediments in the Songnen Plain, then drawing the map of heavy metals by Kriging method. The geo-accumulation index (I geo) and the potential ecological risk index were applied for assessing the status of sediment heavy metal pollution and the extent of potential ecological risk. The spatial distribution map of heavy metal demonstrated that the distribution pattern of heavy mental in lake sediments was that the northeast region was hyper the southwest in the Songnen Plain, the contents of heavy mentals in the city of Daqing, Zhaoyuan, Anda, Qigihar, Dorbod and Nong’an were higher than others areas. The authors indicated that the pollution extent of heavy metals followed the order that Zn>Cu>Ni> Pb>Sr>Mn, Mn was non-pollution and the pollution of Zn had been above mid-level. Combined the geo-accumulation index with the potential ecological risk index, Zn was in mid-level pollution, but in low-level potential ecological risk. The results showed that the Songnen Plain was affected by human activities.