An ecological compensation standard should reflect the value of ecosystem services that their beneficiaries derive from providers. However, as there is no uniform method for the establishment of such standards, we researched the flow of water services in the upper reaches of Miyun Reservoir located in Beijing and Hebei provinces (China) based on the InVEST model and integrated water storage capacity method. The proposed ecological compensation standard can reflect the value of water services flowing from upstream to downstream areas. The results show that the total value of water services in the study area was $62,778.71 × 10⁴/year. The water regulation value accounted for 73.64% of the water service value. Further, the downstream areas in Beijing should pay $57,444 × 10⁴ to the upper reaches. The ecological compensation standards for different supply areas varied based on forest composition. In Chengde, Zhangjiakou, and Beijing, the ecological compensation standards were $759.51/hm²/year, $479.65/hm²/year, and $938.26/hm²/year, respectively. The developed compensation standard reflects the value of the ecosystem services, and is also affordable. The results of this study could thus provide a basis to establish a compensation standard based on continuous consultation and discussion.