The distinguishing and evaluation of natural and anthropogenic sources of heavy metals in soils have always been the important issues in the field of environmental science. In this research, natural sources of heavy metals in soils are calculated according to the relationships between major oxides and heavy metals. The individual sample has independent backgrounds of heavy metals. If the single environmental background is used as baseline, anomalies in regions with low background might be decreased or hided and in regions with high background will be overstated. Enrichment Factor is defined as the ratio of measured concentration and reconstructed background which is of specific significance in practical applications with no assumptions. The agricultural soils near Jilin section of the Songhua River are polluted by Hg seriously with more than half samples over moderate pollutions. The second polluted heavy metal is Cd with half samples moderate pollutions. And individual samples are polluted by Zn moderately. The other heavy metals are almost in the level of background with little human disturbance.