The whole plan of a project may become inefficient because of the inefficiency of its some implementation phase. The traditional DEA model can not beused to deal with such stagewise operation problems. In order to avoid the limitation of the traditional DEA model, a multi-stage DEA model was set up based onthe idea of the DEA model with uncontrollable factor. Simultaneously, considering the shortage of the single DEA model, the multi-stage DEA model was extended to be the multi-objective one. Then, the phase evaluation could be carried out by the multi-stage multi-objectiveDEA model, and the different improve proportions of inputs could be obtained au the same time. The mathematical analysis and numerical simulation results showed that the above mentioned methodology was operable, and the results was more detailed than that using CCR model.