Objective To analyze the dynamic response and strain of the major muscles in head-neck complex of pilot with or without wearing the helmet during carrier aircraft arrested deck landing. Methods Ten-rigid body dynamic model of human head-neck complex was created including head, seven cervical vertebrae and two thoracic vertebrae; mechanical properties of the ligaments, intervertebral discs and other surrounding soft tissues were described by lumped parameter method; mechanical properties of the 15 pairs of muscles in this human head-neck complex were represented by non-linear stress-strain relationship. The model was validated by using experimental data of dynamic responses from the human head-neck complex in a set of different types of automobile crashes. Results The overload curve and strain of this 15 pairs of muscles in head-neck complex of the pilot during arrested deck landing were obtained. The results showed that the extension of splenius cervicis was the largest. The strain of splenius cervicis could reach 50% when the pilot wore the helmet, and it could reach as high as 56% if the helmet’s weight was 2.7 kg. Conclusions Wearing helmet would extend the stretch of neck muscles, and the simulation result could be used for further evaluation on head/neck injury of the pilot.