Carbon sequestration service is transmitted through the atmosphere, and its flow has extraterritorial effects. It not only benefits local areas but also generates spillover benefits in surrounding regions. These spillover benefits are often inadequately assessed, resulting in higher opportunity costs for regions exporting carbon sequestration services, particularly in highly urbanized areas and their surrounding regions. The ecological compensation derived from carbon sequestration flow can explain the relationship between compensation payers and recipients, alleviating the conflicts among stakeholders, and then promoting regional low-carbon development. However, only considering internal flow within a region cannot fully capture the spatial dynamics of carbon flow. Understanding the metacoupling flow mechanism of carbon sequestration both interregional and intraregional and developing ecological compensation strategies are crucial for regional carbon sequestration. Therefore, this study took the Beijing-Tianjin-Hebei (BTH) region of China as the study area. A comparative ecological radiation force model was used to simulate the metacoupling flow of carbon sequestration. On this basis, the carbon compensation amounts were calculated, and the ecological compensation strategies suitable for the region were explored. The results showed that: (1) The supply of carbon sequestration exhibited a spatial distribution pattern characterized by higher in the northwest and lower in the southeast, while the demand showed the opposite trend. Over the past two decades, the total supply decreased, while the total demand increased. (2) The surpluses of carbon sequestration were predominantly located in the western and northern mountain areas, while the deficits were concentrated in the central, eastern, and southern plains. High-high clusters were found in the western and northern areas, while low-low clusters were distributed in a strip extending from the central to the southern regions. Both high-high and low-low clusters expanded over time. (3) The carbon sequestration outflow areas in the BTH initially decreased, followed by an increase from 2000 to 2020. The ranges of the flow expanded initially, then stabilized. The total flows were continuously declining, while the proportion of the long-distance flows transmitted to the regions outside the BTH steadily increased, rising by approximately 6%. (4) In 2010 and 2020, Chengde, Zhangjiakou, Beijing, and Baoding were the main compensation recipients, with total amounts of approximately 718 million CNY and 480 million CNY, respectively. The overall compensation amount declined over time, with Chengde receiving the highest share, while Beijing and Baoding received the least. The proportion of compensation paid by external regions of BTH increased. Future efforts should be focused on analyzing the metacoupling flow of carbon sequestration service from a governance perspective, emphasizing external spillover effects. Meanwhile, with the incorporation of carbon trading markets, the comprehensive ecological compensation policy that integrates both across regions and across different governance levels should be further developed in practice, providing references for the formulation of regional carbon compensation policies and low-carbon development.