In order to ensure safe operation, the China Railway Corporation implemented the principle that Electric Multiple Units (EMUs) and freight trains do not meet in the section on some railway lines when adjusting the train operation chart on June 25, 2021. EMUs and freight trains are prohibited from meetings, which ensures the safety of traffic. However, it will also have a certain impact on operational efficiency. The safety control scheme is added to adjust the train operation plan, so as to avoid the meeting between EMUs and freight trains at the planning level. This paper proposes a quantitative evaluation method for different safety control schemes based on Coloured Petri Nets (CPNs). To exemplify the proposed approach, starting from the dual-track passenger and freight railway, this paper establishes a CPN model to analyze the impact of different safety control schemes on operational efficiency.