In order to correct the inflexibility of the waterfall methodology used in the on-orbit servicing (OOS) satellite ground application system, an iterative software development methodology based on the agile model was proposed. The user was taken to participate the software development process, and the software was kept upgrading to fulfill with the iterative software requirements. The results show that, by using the proposed methodology, the software function would be matched better with the user requirements. Besides that, a reference for improving the future software development efficiencies of the OOS satellite ground application system could be provided from the proposed methodology.