In this paper,a new method to calculate collision risk of air-routes,based on variable nominal separation,is proposed. The collision risk model of air-routes,based on the time variable and initial time interval variable,is given. Because the distance and the collision probability vary with time when the nominal relative speed between aircraft is not zero for a fixed initial time interval,the distance,the variable nominal separation,and the collision probability at any time can be expressed as functions of time and initial time interval. By the probabilistic theory,a model for calculating collision risk is acquired based on initial time interval distribution,flow rates,and the proportion of aircraft type. From the results of calculations,the collision risk can be characterized by the model when the nominal separation changes with time. As well the roles of parameters can be shown more readily.