The ecological compensation standard in transboundary river basins should be determined by the basin countries through negotiation on the basis of the base value of the ecological compensation standard. This paper calculated the base value range of the ecological compensation standard, determining the upper limit based on the spillover value of ecosystem services for the ecosystem-service-consuming country and the lower limit according to the cost of ecological protection for the ecosystem-service-supplying country. The final range was determined by integrating this with the willingness to pay and the actual effort in each basin country. Taking, for example, the Lancang–Mekong River basin, the results indicate that the spillover value of ecosystem services in Laos, China and Myanmar was positive and these three countries were ecosystem-service-supplying countries, while in Cambodia, Vietnam and Thailand it was negative and these three countries were ecosystem-service-consuming countries. Among the ecosystem-service-supplying countries, the cost of ecological protection of them was in descending order of Laos, China and Myanmar, which was related to their own level of economic development. Considering the adjustment coefficient for the payment of ecosystem service value and the cost-sharing coefficient of each basin country, the feasible range for the base value of the ecological compensation standard was determined to be [2.47, 229.67] × 108 $, which provided the basis for the negotiation on the determination of the ECS. In addition, implementation suggestions were proposed from three aspects: establishing a basin-information-sharing mechanism and platform, establishing an integrated management organization for transboundary river basins, and strengthening and improving the coordination and supervision model of ecological compensation.