<p>City clusters are key spatial units for achieving China’s carbon peaking and carbon neutrality goals, and their internal embodied carbon transfer mechanisms determine the effectiveness of coordinated emission reduction and system resilience. Taking the Pearl River Delta (PRD), a national-level mega-city cluster, as a case study, this study integrates a multi-regional input-output model with complex network theory to construct an embodied carbon transfer network and evaluate system robustness through perturbation scenario simulations. The results show that the PRD embodied carbon transfer network exhibits typical small-world and scale-free properties and forms a core-periphery structure dominated by a small number of sectors, particularly those related to energy and construction. During the study period, the network underwent simultaneous expansion in scale and improvement in topological efficiency, while structurally evolving from a polycentric configuration toward an integrated structure. The hub functions of advanced manufacturing and service sectors also strengthened markedly. Risk assessment shows that the network is robust to structural disruptions targeting intermediary hubs but relatively sensitive to shocks that impose aggregate constraints on high-carbon-flow nodes. Temporal comparison further shows that overall network resilience increased over time. The integration process of the PRD city cluster did not improve efficiency at the expense of system resilience; rather, it achieved synergy between network efficiency and resilience. These findings provide an empirical basis for formulating differentiated coordinated emission reduction policies.</p>