Ecological compensation is one of the important measures to coordinate regional ecological protection and economic development. As the only inter-provincial river in Fujian Province and the second inter-provincial watershed of the eco-compensation pilot in China, the Tingjiang River basin has attracted increasing attention from policy makers and scholars. This study aims to systematically analyze the ecological compensation mechanism and improve the effectiveness of ecological protection in the Tingjiang River basin. In this paper, ecosystem service value (ESV) is used as a criterion for establishing ecological compensation standards. Based on the land cover datasets from 2010 to 2020, the spatial distribution and the dynamic changes of ESV were determined. Subsequently, the priority and standards of ecological compensation were established according to the level of the socio-economic development. Finally, the horizontal ecological compensation was determined by combining the actual benefits and willingness-to-pay of downstream beneficiary regions. The results indicate the following findings: (1) The ESV of the Tingjiang River basin exhibited a decreasing trend over the past decade. It decreased from CNY 70.72 billion in 2010 to CNY 69.05 billion in 2020, with a rate of change of −2.37%; (2) The growth of GDP in the research area has led to a decrease in the priority and standards of ecological compensation. The ecological compensation quota shows a decreasing trend from upstream to downstream, that is, Changting county (33%) > Wuping county (27%) > Shanghang county (21%) > Yongding district (19%); (3) The amounts of horizontal ecological compensation that Guangdong province need to pay are CNY 224 million, 166 million, and 109 million in 2010, 2015, and 2020, respectively. The findings of this research can not only optimize the allocation of ecological compensation, but also provide a reference for other countries/regions to carry out relevant research work.