Aiming at the problems of single compensation standard and incomplete compensation content in cross-border ecological compensation, this study takes the Xin'an River Basin as an example, builds a dynamic measurement model based on opportunity cost method and ecosystem service value method, and carries out cross-border ecological compensation standard research. According to the current agreement on the water quality of the Xin'an River Basin, the ecological compensation is divided into two trial phases: trial and restoration. The compensation period fall in 2012-2014 and 2015-2017 respectively. Opportunity cost method is used in the trial phase, and ecosystem service value method is used in the restoration phase. The results showed that: (1) the direct and indirect cost quotas for ecological compensation in the Xin'an River Basin in the pilot phase increased from 1.849 billion yuan and 228 million yuan in 2012 to 3.247×10⁶ yuan and 401×10⁶ yuan in 2014, respectively. Among them, the averagely annual ratio of industrial indirect costs was as high as 55.10%, which indicated that Huangshan City has gradually strengthened the ecological management and investment of the river basin from various aspects, especially the polluting enterprises that had a direct impact on the aquatic ecological environment of the river basin. (2) The amount of ecological compensation in the Xin'an River Basin also showed an upward trend from 2015 to 2017. The annually average increase in the total supply and self-consumed ecosystem service value of Huangshan City were 5.08% and 4.32%, and the total supply of ecosystem service value was 0.76% higher than its own consumption, which reflects that Huangshan City has improved the quality of the water ecological environment of the river basin by increasing the ecological area and changing the type of land use etc. (3) The total amount of ecological compensation in the pilot phase of Xin'an River Basin from 2012 to 2014 was estimated at 8.067 billion yuan, and the total amount of ecological compensation in the restoration phase from 2015 to 2017 was estimated at 12.565 billion yuan. However, the actual amount of ecological compensation amounted to 3.6 billion yuan since the pilot of the Xin'an River Basin was much lower than the upstream investment and loss in environmental improvement. Therefore, in order to protect the ecological environment of the Xin'an River Basin, we recommended that both sides of the basin established a dynamic and long-lasting ecological compensation mechanism to increase the amount of ecological compensation.