The non-contact close-proximity formation satellite (NCCPFS) is one of the technical solutions to improve the attitude performance, consisting of a payload module (PM) and a support module (SM). The non-contact Lorentz actuator (NCLA), as the core components of the NCCPFS, directly affect the attitude control performance of the entire satellite. In order to ensure the ultra-high attitude pointing performance and stability of the PM, an in-flight calibration method for the NCLAs based on minimum model error (MME) algorithm and Kalman filtering (KF) with cooperative control strategy is proposed in this article. In this method, the NCLAs generate a periodic nominal torque that causes the attitude of the PM to be periodically deflected. This periodic torque also reacts on the SM, and the SM counteracts this periodic torque through the flywheel to realize the cooperative tracking relative to the PM. Then, the gyroscope data are substituted into the MME algorithm to obtain the angular acceleration of the two modules, and the KF algorithm is adopted to observe the actual output torque of the NCLAs to complete the in-flight calibration of the NCLAs. Numerical simulation results show that the accuracy of the proposed calibration algorithm can reach about 8%, which proves the effectiveness of the proposed method.