Korea introduced the cooperation charge on conservation of ecosystem for minimizing damage of ecosystem due to development projects and their effects and for preparing resources for natural environment conservation projects. Advanced countries have made efforts by expanding investment in natural environment conservation and restoring projects to promote prevention of global warming and improvement of biological diversity, are establishing nationwide strategies and plans. To examine the reality of projects by returns of the cooperation charge on conservation of ecosystem, microsite projects in schools and public facilities take the largest share while their project budgets are only about 100~300 KRW, relatively small, which might be attributable to budget restrictions in accordance with the calculating method of levying cooperation charge on conservation of ecosystem and problems of project proceeding in the system of returning fund for projects in general. The conclusion which this study suggests on invigoration of cooperation charge on conservation of ecosystem and its operation are as followings. First, although the cooperation charge on conservation of ecosystem has been introduced in 2001, the amount of imposition per unit area remains unchanged. It is desirable to increase the amount into $1,400KRW/m^2$ as of August, 2011 as the price index has been continuously rising for the past 10 years and the upward adjustment of imposition per unit area should be notified by the decree of the Ministry of Environment every January. Second, the ceiling amount of the cooperation charge on conservation of ecosystem should be abolished. Now the ceiling amount is defined as 1 billion KRW but it was found that there was not any ceiling amount specified according to the comparative analysis of similar systems with the Korean environmental improvement fund. The ceiling should be abolished so that medium level businesses are carried out and ecosystem recovering projects in the true sense of the word can be made smoothly. Third, weight should be introduced in calculating amounts in accordance with ecologic and economic values. Harmony between development and environment can be achieved by applying differentiated weights of constant regional coefficient by use zone and ecologic and economic values. Continuous efforts of improving cooperation charge on conservation of ecosystem should be made more than anything else so that projects by returns of cooperation charge on conservation of ecosystem get effectiveness.