The interdependence of different energy forms in multiple energy systems (MESs) could leverage their synergies to reduce carbon emissions. However, such synergies cannot be exploited without the right incentives. This paper studies the low-carbon operation of MESs by coordinating the transmission-level and distribution-level via the energy-carbon integrated prices. Energy prices are decided by locational marginal pricing principles in the transmission-level MES. At the same time, the carbon emissions of different energy systems are uniformly priced using a carbon emission flow (CEF) model based on the consumers’ actual emission contributions by tracing the embedded flow of CO2. Various distribution-level MESs modeled by energy hubs (EHs) are independently operated in response to the variation in the integrated prices. The whole bi-level model formulates an equilibrium problem and is solved iteratively. Case studies based on two MESs at different scales illustrate the effectiveness and benefit of the proposed carbon pricing method in reducing carbon emissions more efficiently than current methods.