Resonable river naturalaess evaluation has a positive effect for exploting soil and water resources. Meanwhile, it plays an active role in soil and water consercation. We established a naturalness evaluation system of rivers in Beijing mountainous areas which consists of 23 qualitative and quantitative indexes. The analytic hierarchy process (AHP) is used to determine the weight of each index. We classify the rivers in Beijing mountainous areas into five grades: natural state, nearly natural state,degraded state, seriously degraded state and artificial state. In order to improve the evaluation efficiency,we developed the evaluation system using Java language, with five-element connection number as the evaluation model. The system realizes procedural evaluation process. It also provides scientific support for the river managers to analyze problems or to take ecological restoration measures. Based on the data in 2008 and 2011, we assessed the naturalness of Andamu river using the system. The results show that evaluation grade of Andamu Rive is on the decline on the whole, and that of nine out of the totally 16 samples drops to different degrees. The nine samples are all adjacent to villages greatly influenced by human activities.