This study simulated the nanofiltration (NF) process of contamination removing by back-propagation neural network (BPNN), according to the test values of DK membrane pre-treating Imidacloprid pesticide wastewater. The real time nanofiltration (NF) separation model was presented for effective controlling of DK NF separation. The research showed the simulation precision met the application demands, with the correlation coefficient between the simulation and test rejection of COD and salt over 0.99, and absoluteness error below ±4%. In order to test the prediction of this BPNN simulation model, further NF experiments were carried out. Under the same multifactor condition, the predictions for the NF process performances were found to be in good agreement with the experimental results. This BP simulation model for NF process could be used to test the stability and effectively of NF system, and support the membrane technology well.