The effectiveness of rapid rail transit system is analyzed using tools of complex network for the first time. We evaluated the effectiveness of the system in Beijing quantitatively from different perspectives, including descriptive statistics analysis, bridging property, centrality property, ability of connecting different part of the system and ability of disease spreading. The results showed that the public transport of Beijing does benefit from the rapid rail transit lines, but there is still room to improve. The paper concluded with some policy suggestions regarding how to promote the system. This study offered significant insight that can help understand the public transportation better. The methodology can be easily applied to analyze other urban public systems, such as electricity grid, water system, to develop more livable cities.