The health status of Naolihe Basin has already varied significantly affected by the climate change and human activity. Therefore, it is reasonably much important to analyze and evaluate the health status of river, which could provide basis for the comprehensive development and protection in the Naolihe Basin. So, this paper takes Baoqing country as the study region, uses the stable state, the harmonious degree and evolution rate to describe the health status, and establishes the health evaluation index system of water-based system in Baoqing country based on the concept of water-based system. The entropy method is used to the weight vector of steady state index and harmonious degree index, the TOPSIS was applied to analysis the health status of water-based system of Baoqing country during 2005 to 2009. The comprehensive evaluation result shows that the water-based system of Baoqing country is in the state of comparative healthy, the main reason is that water resources of the study area are relatively insufficient, and drinking water security and water consumption cannot obtain the complete guarantee, which leads to lower steady state.