With the increasingly busy operation of civil aviation airspace, the possibility of flight conflict on air route increases. From the perspective of quantitative analysis, how to build an effective and reasonable mathematical model for the quantitative assessment of flight collision risk on air route, improve the scientificity of air route planning and management, and build an effective and reasonable mathematical model for the quantitative assessment of flight collision risk on air route is a problem facing the industry. An improved Event model based vertical collision risk assessment method for flight route is proposed. In this method, the cuboid in the original Event model is replaced by two elliptical cones which correspond to the velocity vector distribution of the aircraft in space. The probability of the aircraft passing through the adjacent altitude layers is calculated, and the vertical collision risk value of the aircraft in the improved route is derived from the ratio of the area size of the collision box before and after the improvement. Calculation examples show that the vertical collision risk of the improved method is about 50% of that of the original cuboid Event model, and 60% of that of the original ellipsoid Event model. The improved collision risk model is more reasonable and feasible.