We　propose　a　one-step　scheme　for　implementing　multi-qubit　phase　gates　on　microwave　photons　in　multiple　resonators　mediated　by　a　superconducting　bus　in　circuit　quantum　electrodynamics　(QED)　system.　In　the　scheme,　multiple　single-mode　resonators　carry　quantum　information　with　their　vacuum　and　single-photon　Fock　states,　and　a　multi-level　artificial　atom　acts　as　a　quantum　bus　which　induces　the　indirect　interaction　among　resonators.　The　method　of　pulse　engineering　is　used　to　shape　the　coupling　strength　between　resonators　and　the　bus　so　as　to　improve　the　fidelity　and　robustness　of　the　scheme.　We　also　discuss　the　influence　of　finite　coherence　time　for　the　bus　and　resonators　on　gate　fidelity　respectively.　Finally,　we　consider　the　suppression　of　unwanted　transitions　and　propose　the　method　of　optimized　detuning　compensation　for　offsetting　unwanted　transitions,　showing　the　feasibility　of　the　scheme　within　the　current　experiment　technology.　©　2020　Optical　Society　of　America　under　the　terms　of　the　OSA　Open　Access　Publishing　Agreement.