In view of the lack of security assessment methods of LTE-R communication systems in high-speed railway and the fuzziness and gray of the evaluation process, this study develops a risk assessment model for LTE-R communication systems based on set pair extension and improved analytic hierarchy process. The evaluation system is established mainly from the aspects of people, equipment, and networks that affect the communication system, and the risk assessment indicators and evaluation standards are determined. The improved analytic hierarchy process is used to calculate the weight, construct the system risk set pair via the set pair extension and calculate the risk connection membership degree to judge the risk level of the communication system. The analysis of an example shows that the use of set pair extension and improved analytic hierarchy process can effectively and truly reflect the risk state of LTE-R communication systems and can provide a theoretical basis for their security construction and risk control.