China has been undergoing a rapid process of urbanization. The urbanization rate, increased from 35% in 2000 to 59.58% in 2018, and is expected to increase to 70% by 2030. As Chinese cities consumed approximately 77% of China’s total energy and emitted about 81% of all carbon emissions in 2017, it has become increasingly necessary to quantitatively analyze city-level carbon emissions and related issues. The present study adopted single regional and multi-regional input-output (MRIO) models to analyze the features of four Chinese municipalities (Beijing, Tianjin, Shanghai and Chongqing) and calculate their embodied carbon emissions (ECE). In addition, we used ecological relationship concepts to analyze the relationships between those municipalities and other regions based on ECE flows through an ecological network analysis (ENA) model. The results show that all four megacities were net importers of ECE, and their imported ECE typically flowed from nearby geographic regions. In addition, exploitation was the main ecological relationship between these four megacities and China’s other regions. Knowing the detailed data related to ECE, ECE flows and the ecological relationships among these megacities could help policymakers establish more comprehensive environment-related policies, which are crucial for achieving sustainable development targets.