Abstract: In order to assess the extent of heavy metals contamination resulting from geo-authentic productive area of Ligusticum chuanxiong Hort. in Sichuan province, fifteen soil samples were collected and analyzed for the content of the heavy metals. The assessment of heavy metals contamination in soils was performed by double-layer back propagation neutral network and GIS spatial analysis technology. The results of assessment indicated that most of research area was contaminated lightly. The areas of Chouzhou, Dujiangyan and Pengzhou were polluted in middling extent. The way of double-layer BPNN and GIS could carry out a relatively accurate spatial analysis to even a small group of data, reduce the cost of sampling under the principia of a stated analysis precision and get higher accuracy spatial distribution than the single-factor index method.