The calculation of ecological compensation standard and the allocation of funds are the key and difficult problems in the establishment of trans-provincial water ecological compensation mechanism. It is necessary to calculate the direct cost compensation and the opportunity loss compensation respectively according to different characteristics of compensation, and then allocate the direct cost compensation to various districts and counties in the water source areas. The model for calculating the compensation amount and the entropy weight model for the allocation of funds based on the transprovincial cross-section water quality and investment benefits are established. Taking the pilot project of trans-provincial compensation mechanism in Dongjiang River Basin as an example, the annual compensation amount of water ecological protection in the source area of Dongjiang River in Jiangxi Province is 3． 186 billion yuan, among which the direct cost compensation is 1． 106 billion yuan, which is distributed to Xunwu County, Anyuan County and Dingnan County according to the proportion of 37． 2%, 32． 2% and 30． 6%. The results are higher than the compensation amount of “ Agreement on horizontal ecological compensation for the upper and lower reaches of Dongjiang River Basin”, which can provide support for optimizing the compensation standard and utilization of funds of trans-provincial water ecological compensation in China and implementing differential compensation mode.