The Beijing new airport project is developed to satisfy the aviation demand of Beijing area. There are 4 runways in the new airport, as well as two alternative programs in the present period, which are called “3+1” and “4+0” to differentiate. Through macro analysis from airport administration, air traffic control and airlines, the evaluation system for choices of alternative program is established, which includes runway capacity, ground taxing time and delays. Then, the theory runway capacity is estimated. After the analysis of these, this paper builds the separate model based on the Simmod software. The “3+1” program is a better option based on the simulating models and the evaluation system. Besides, the conclusion could give theoretical reference to research for the runway layout comparison of Beijing new airport.