The damage caused by the lupus nephritis to the patient's kidney was very little studied for treatment module; however, we have the understanding the disease involving in the kidneys by an immune complex glomerulonephritis. Human genomics have been decoded since 2004, it should give clinical scientists and medical doctors a new scenery to develop some new treatment modules to cure these kinds of patients. Here we used a group of genomic data from lupus nephritis to combine the modern medicine knowledge and Traditional Chinese Medicine (TCM) so that an integration module will be subject to the clinical field. The integration model is primarily relied on a comprehensive regulation mechanism of system biology including network, topology and gene-drug interaction database. In this manual we first study the role using genomic expression signature from several databases of clinical lupus nephritis, and then we combine current medications with their immune suppress treatment and TCM with their theory and medication in order that the integration model was eventually established. In near future, we will extend a second-generation model based on the module by using a set of clinical genomic data from different patients such as individual patient genomic data, each patient symptom, laboratory results.