The Flexible Atomic Code (FAC) is developed to extend the computational scale based on the Relativistic Configuration Interaction (RCI) in the theoretical study of W9+ atomic structure. The results of the lowest 144 energy levels are consistent with the GRASP calculations, with a mean deviation of 2.11 %. The reference configuration selections for central potential optimization in the RCI calculations at different computational scales are studied. The contributions of the inner core 4d to the energy levels of the RCI calculations are also investigated. The mean deviation of the theoretical wavelengths of five M1 transitions of W9+ from the experimental results is within 0.86 %. This work demonstrates the feasibility of improving the accuracy of RCI calculations of complex atomic systems through large-scale computation based on FAC, which is helpful for experimental spectral line identifications and spectrum synthesis in many fields of plasma spectroscopy.