For the purpose of establishing a safety assessment method, a new trains control system for a single-track line is analyzed from the viewpoint of safety and effectiveness by means of a Petri net modeling analysis. Software safety is the most important and a difficult problem to assure of system safety. To overcome this difficulty a new method named skeleton-check method is introduced. The method, which is a more economic and convenient design diversity method using the output from the specification validation process, generates a skeleton-check routine independent of the application programs. The merit of the method is being able to find errors made by deviating from the specification, because of being always confirmed that the movement of the system is in the specification validation process.