Accurately identifying ecological compensation areas and scientifically determining appropriate compensation amounts are crucial for establishing a robust ecological compensation mechanism, which in turn is key to promoting the coordinated development of ecological protection and high-quality economic growth. This study innovatively proposes a framework for ecological compensation termed “Accounting of Ecosystem Services Value–Identification of Priorities for Payers and Recipients–Calculation of Ecological Compensation Amount (ESV–PPR–ECA)”. It utilizes the InVEST model and the emergy method to assess the value of ecosystem services, constructs the Ecosystem Payment and Recipient Priority Sequence (EPRPS) Model to identify the payers, recipients, and their priorities for ecological compensation, and employs the conversion factor method to calculate the Ecological Compensation Amount (ECA). This framework aims to address the questions of “How should compensation be provided?”, “Who should compensate whom?”, and “How much compensation is necessary?”, ensuring the optimal use of ecological compensation funds and providing a scientific basis for inter-regional ecological compensation. The study’s findings indicate that the total Ecological Compensation Amount for the Yellow River Delta in 2020 was 3.848 billion RMB, with the total amount receivable being 4.032 billion RMB and the total amount payable being 184 million RMB. The compensation funds should be prioritized for tideland and the Yellow River, and venture, cropland and industrial land should be the first to contribute compensation. Additionally, the Ecosystem Service Value of the Yellow River Delta showed a declining trend from 2015 to 2020, underscoring the urgent need to establish a horizontal compensation mechanism for the region. Such a mechanism would incentivize environmental protection and the construction of ecological civilization, ultimately enhancing ecosystem service functions. Therefore, we recommend the implementation of horizontal fiscal transfers, where financial assistance is provided from paying areas to recipient areas, offering a scientific reference for the establishment of a horizontal compensation mechanism within the Yellow River Delta.