The dynamic model of flexible multi-body spacecraft with topological tree configuration has been established based on the Lagrange’s equations in terms of quasi-coordinates.The kinematics of the spacecraft is described by Modified Rodrigues Parameters(MRPs).For this time-varing uncertainty flexible multi-body spacecraft dynamic system,a modified fractal controller via variable universe of discourse was designed and the numerical simulation was done.The results show that this control scheme avoids the flaw caused by real-time calculating of shrinkable factors,realizes the effective control of flexible multi-body spacecraft for large angle attitude maneuver,and assures the vibration suppression of the spacecraft flexible appendages at the same time.