Background <p>High-resolution carbon emission checking and the tracking of carbon flows within and between cities are crucial for carbon emissions reduction and regional coordinated development. However, current research in both directions remains insufficient and requires further exploration. This study selected two big and tight interacted cities from the urban agglomeration along China’s longest and largest river. The research employs two methodologies, the first monitors carbon emissions in high resolution and the second checks the indirect carbon flow hotspots between the two cities.</p> Results <p>Results found that both cities showed a significant increasing trend for total carbon emissions from 2000 to 2020. The peak for Nanjing was in 2018, 2648.09 × 10⁴ t, and Changsha’s peak was in 2017, reaching 2202.51.15 × 10⁴ t. Industry is always the main contributor to carbon emissions, but the percentage is decreasing. Generally, carbon emissions in Nanjing are distributed more spatially intensively than in Changsha. There was a similar regularity of carbon emissions for both cities from urban residential, commercial and traffic sectors Through population flow and trade, Changsha pulled 2.65 × 10⁴ t carbon emissions in Nanjing, and the reversed amount that Changsha pulled in Nanjing is 1.87 × 10⁴ t. Generally, Nanjing has a slight advantage over Changsha regarding the higher carbon emissions produced there</p> Conclusions <p>This research holds significant implications for the development of low—carbon cities and the promotion of coordinated regional development.</p>