In satellite formation flying systems, replay attacks can evade detection by intercepting and transmitting legitimate historical data to formation satellites, which causes serious threats to the normal operation of satellite systems. Considering the satellite formation flying system of which the kinematics is described as the Clohessy-Wiltshire equations, this paper presents a method of replay attack detection based on a Chi-square detector and physical watermarking. In order to easily detect the replay attacks by utilizing the Chi-square detector, a model of Gaussian watermark noise is established. This method significantly enhances the outputs of the Chi-square detector under replay attacks without altering the detector’s threshold at the cost of some formation flying performances. This provides theoretical support for the detection of replay attacks and the timely defensive security of satellite formation flying systems. Finally, simulation results illustrate the presented method.