The stellar refraction navigation is a type of autonomous celestial navigation method for satellites that uses high-accuracy star sensors to obtain the stellar refraction. The apparent height and the stellar refraction angle are two kinds of measurements for the satellite stellar refraction navigation system. A better navigation performance can be achieved by the stellar refraction angle rather than the refraction apparent height. However, the measurement model of the stellar refraction angle is an implicit function, which needs an implicit filter method. A new implicit unscented Kalman filter (UKF) method is proposed and applied to the satellite stellar refraction navigation system in this paper. The main difference between the classical UKF and the implicit UKF lies in the measurement update. First, since the implicit measurement model can be rearranged into an equation whose one side is zero, the vector of zeros is regarded as the equivalent measurement, and the difference between the predicted measurement and its true value is utilized for updating the predicted state and its covariance matrix. Second, the measurement noise and its covariance matrix are transformed based on the unscented transformation principle. In addition, the implicit UKF is compared with the implicit extended Kalman filter (IEKF), the iterative IEKF, and the UKF. Simulations show that the proposed implicit UKF method can obtain about 19.0% and 17.5% improvements in three-dimensional root mean square position estimation compared to the IEKF and the iterative IEKF, respectively. Although the navigation performance of the UKF is close to the implicit UKFs, the computational time of the implicit UKF is much shorter than the UKFs. In addition, the sensitivities of the four different Kalman filters to the star sensor's faults and the atmosphere perturbation are compared, respectively.