This paper investigates the issues of iterative learning algorithm-based robust thruster fault reconstruction and reconfigurable fault-tolerant control for spacecraft formation flying systems subject to space perturbations. Motivated by sliding mode methodology, a novel iterative learning observer (ILO) was developed to robustly reconstruct the thruster faults. Based on the fault signals obtained from the ILO, a learning output–feedback fault-tolerant control (LOF²TC) approach was explored such that the closed-loop spacecraft formation configuration was accurately maintained in the presence of space perturbations and thruster faults. Numerical simulations were employed to demonstrate the effectiveness and superiority of the proposed ILO-based fault-reconstructing approach and LOF²TC-based configuration maintenance approach for spacecraft formation flying systems.