To reduce the collision risk to civil airliners caused by suborbital vehicle disintegration events, this paper uses a covariance propagation algorithm to model the debris landing point of suborbital disintegration accidents and gives a collision probability analysis method for civil airliners encountering debris during the cruise. Collision warning is performed for airborne risk targets to improve the emergency response capability of the ATC surveillance system to hazardous situations. The algorithm models the three-dimensional spatial motion target localization problem as a Gauss-Markov process, quantifying the location of debris landing points in the vicinity of nominal trajectories. By predicting the aircraft trajectory, the calculation of the inter-target collision probability is converted into an integration problem of a two-dimensional normally distributed probability density function in a circular domain. Compared with the traditional Monte Carlo method, the calculation speed of debris drop points is improved, which can meet the requirements of civil aviation for real-time response to unexpected situations.