As one of three civil aviation systems, the Air Traffic Management (ATM) system plays a very important role in security of civil aviation. This paper established the safety risk evaluation index system for ATM. According to the Gray Relational Analysis (GRA), the paper calculated the correlation coefficients and correlation degree between the safety risk in ATM and the first level factors, and the correlation coefficients and correlation degree between the first level factors and corresponding second level factors. The results show that human factor which has been greatly impacted by poor safety awareness contributes main reason to safety risk in ATM. This paper provides ATM units with recommendations to establish risk management programs.