Based on molecular profiling, several prognostic markers for HCC are also used in clinic, but only a few genes have been identified as useful. We collected 72 post-operative liver cancer tissue samples. Genes expression were tested by RT-PCR. Multilayer perceptron and discriminant analysis were built, and their ability to predict the prognosis of HCC patients were tested. Receiver operating characteristic (ROC) analysis was performed and multivariate analysis with Cox's Proportional Hazard Model was used for confirming the markers'predictive efficiency for HCC patients'survival. A simple risk scoring system devised for further predicting the prognosis of liver tumor patients. Multilayer perceptron and discriminant analysis showed a very strong predictive value in evaluating liver cancer patients'prognosis. Cox multivariate regression analysis demonstrated that DUOX1, GLS2, FBP1 and age were independent risk factors for the prognosis of HCC patients after surgery. Finally, the risk scoring system revealed that patients whose total score >1 and >3 are more likely to relapse and die than patients whose total score ≤1 and ≤3. The three genes model proposed proved to be highly predictive of the HCC patients' prognosis. Implementation of risk scoring system in clinical practice can help in evaluating survival of HCC patients after operation.