Objective The finite element method was used to simulate the dynamic response of pilot's cervical spine during typical maneuvering flight movements, and the neck injury of human body during flight was analyzed and predicted by the impact injury and fatigue injury model of biological tissue. Methods A geometrically accurate finite element model of neck was constructed, and the validity of the model was verified by relevant examples. Then, the acceleration curves of centrifugal trainer during different modes were loaded to numerically simulate, and the impact damage and fatigue damage of tissue were predicted by using the universal cervical injury criterion and the fatigue damage model of biological tissue. Results The results show that the maximum stress of vertebrae and intervertebral disc is 66.53MPa and 58.63MPa respectively during the typical maneuverable flight. According to the NIJ injury criteria, the maximum value was 0.096, which was lower than the injury tolerance threshold of 1, and would not cause direct acute injury to the cervical spine bone tissue. Based on the fatigue damage model of biological tissue slices, it was found that cancellous bone suffered fatigue failure under the condition of uninterrupted repeated loading for more than 40,000 times. Considering the limited flight career of the pilot, the vertebral bone tissue would not be damaged due to the accumulation of fatigue damage. Conclusions In this paper, the dynamic response of the pilot’s neck during typical maneuvering flight is simulated, combined with the biological tissue damage model to predict the impact and fatigue damage of the pilot’s cervical spine respectively. To a certain extent, it helps to formulate pilot training and flight plans, and also provides data support for the development of its protective equipment.