In this paper, the thermal analysis of a membrane antenna structure is performed, and then, the rigid-flexible coupling dynamic modeling and control of the membrane-antenna-satellite system are studied with the thermal stress considered. The thermal analysis model of the membrane antenna structure is derived based on the finite element method by discretizing the structure into 1D and 2D thermal elements. Considering the thermal stress, the vibration modes of the membrane antenna structure are obtained, and the rigid-flexible coupling dynamic model of the membrane-antenna-satellite system is derived based on the hybrid coordinate method. To reduce the vibration of the membrane antenna structure caused by the attitude maneuver, the control command is designed based on the component synthesis vibration suppression (CSVS) method. Simulation results show that the dynamic properties of the membrane antenna structure are affected significantly by the space thermal environment, the vibration of the membrane antenna structure can be suppressed effectively by the presented CSVS controller, and the accuracy of the attitude maneuver will be improved significantly by the proposed control strategy.