This paper focuses on the vibration control problem of the space truss by rejecting the external disturbance that not only matched but also unmatched based on the Equivalent-Input-Disturbance (EID) approach. The finite-element analysis (FEA) is utilized to calculate the mass matrix, damping matrix, stiffness matrix and input matrix to model the space truss. For convenient analysis and synthesis, the modal truncation is introduced to reduce the order of the model of the space truss, which is a high order system. Furthermore, a novel and effective EID observer is constructed to observe the external unknown disturbance, which is the main reason of the vibration of the space truss. Adaptations of these, a vibration control scheme that utilizes the observation results is proposed for the space truss. Finally, numerical examples, which show the method in this paper can reject external unknown disturbance, are provided to illustrate the effectiveness of the proposed methods.