The purpose of this article is to find a better way of “holistic ecological mission of NGO” and restoration of global’s environmental crisis from studying the ecological mission of NGO in view of the principle of mutual prosperity in of Unification Thought. Today, because the global environmental crisis is at its highest point due to neoliberalism, the church should actively participate in the efforts to protect the ecosystem by missionary work of NGO. Therefore Family Federation for World Peace and Unification(FFWPU) is doing a lot of work to alleviate global poverty, education problems, and overcome the environmental crisis. NGO ecological mission is typically holistic mission model NGO, it will revive the depressed Korean Church by protecting the environment and doing missionary work at the same time. For an effective activity of holistic ecological mission of NGO, the following conditions are required : Firstly, The role of the Church in the ecosystem should be more coordinated. Political co-prosperity, preservation of the ecological environment, quality of life, and the restoration of the soul can be considered as the holistic ecological mission of NGO. Secondly, for understanding the situation of missionary areas in holistic ecological mission of NGO, we need mutual prosperity for NGO’s citizen engagement from the contradiction that is simply biased to the political aspects. Thirdly, facing the crisis of the world environment ecosystem, our lives must be able to essentially paradigm shift to Heavenly Parents through ecological theology and ecological mission of NGO. lastly, the proclamation of gospel is also important in the establishment of church, but we should approach it with a holistic mission model on urgent matters such as the environmental ecosystem crisis in the community. In other words, we need to take a stance to create a community with the local people in the course of action with holistic ecological mission of NGO.