Air-breathing hypersonic vehicles have capabilities of hypersonic speed and strong maneuvering, and thus pose a significant challenge to conventional tracking methodologies. To achieve desirable tracking performance for hypersonic targets, this paper investigates the problems related to measurement model design and tracking model mismatching. First, owing to the severe aerothermal effect of hypersonic motion, an infrared measurement model in near space is designed and analyzed based on target infrared radiation and an atmospheric model. Second, using information from infrared sensors, a composite tracking algorithm is proposed via a combination of the interactive multiple models (IMM) algorithm, fitting dynamics model, and strong tracking filter. During the procedure, the IMMs algorithm generates tracking data to establish a fitting dynamics model of the target. Then, the strong tracking unscented Kalman filter is employed to estimate the target states for suppressing the impact of target maneuvers. Simulations are performed to verify the feasibility of the presented composite tracking algorithm. The results demonstrate that the designed infrared measurement model effectively and continuously observes hypersonic vehicles, and the proposed composite tracking algorithm accurately and stably tracks these targets.