Abstract: Cross-regional horizontal ecological compensation is a crucial approach to implement the strategy of ecological civilization and establish a positive interactive relationship between ecological protectors and beneficiaries. Ecosystem service flow clearly reflects who, when, and where benefits from ecological services, which is a new focal point for research on cross-regional horizontal ecological compensation. Based on the quantitative assessment of ecosystem service quality and value in the Wuhan metropolitan area for the year of 2000, 2010, and 2020, this study unveiled the spatial flow characteristics of ecosystem services. Furthermore, this paper constructed a cross-regional horizontal ecological compensation model by adjusting the value transfer amount and incorporating the socio-economic development level coefficient. The results showed that: (1) The spatial dislocation of ecosystem service supply and demand in Wuhan urban agglomeration was obvious. (2) Ecosystem service flows were primarily directed towards the northeast and southwest regions with an overall increasing trend in flow radius, intensity, and value transfer. (3) The total amount of ecological compensation increased continuously from 1.452 billion yuan to 2.452 billion yuan in 2000, 2010 and 2020. Thee amount of compensation for each compensation area increased from 0-823 million yuan to 0-1 065 million yuan, and the amount of compensation for each compensation area increased from 0-948 million yuan to 0-1 147 million yuan.