The performance of high precision payloads on board a satellite is extremely sensitive to vibration. Especially, vibration disturbance from the reaction wheel assembly (RWA) could cause serious problems in spacecraft missions. To protect the high precision payloads from the RWA disturbance, vibration isolators are often applied in the vibration propagation path. The vibration isolator for RWA disturbance is typically designed without considering the flexibility of the structures. The vibration isolator for RWA could be better designed by considering the the flexibility of the satellite structure. In this paper, the three parameter isolator is designed to reduce the RWA disturbance considering flexible structural effects. The RWA disturbance in a flexible mount is predicted with the transfer function which depends on the estimated interface accelerances of the RWA and the spacecraft structures. Finally, the isolation performance of the designed isolator is compared for two conditions: the RWA disturbance in a hard mount condition and in a flexible mount condition.