Abstract: To address the existed problems of ecological compensation standard for opportunity cost, and according to the trans-regional eco-compensation calculating model of Minjiang River Basin which is based on opportunity cost. This paper statistical classified the ecological protection costs of the 2010-2015 in the upper reaches, and has confirmed the amount of compensation that should be paid to the upper reaches of the Minjiang River basin in the light of economic development level in the lower reaches. The results indicated that the amounts of eco-compensation received by Sanming and Nanping cities were 0.5694×10⁸~0.9407×10⁸ Yuan and 2.0104×10⁸~2.7061×10⁸ Yuan, respectively. The downstream Fuzhou city needed to pay 2.5797×10⁸~3.4913×10⁸ Yuan for eco-compensation. Corresponding to it, some countermeasures are put forward as suggested:Expending compensation financing channels, combination the compensation model government-led and market. Besides the financial compensation, the project compensation or technical compensation were also discussed in this article.