Industries are undergoing low-carbon evolution with worldwide awareness of energy conservation. As the super key to processing it, integrated energy systems (IESs) are receiving more attention, in terms of cutting carbon emissions actively and passively. Until now, many well-established strategies have been proposed to low-carbonize IESs. However, issues still remain in implementing low-carbonization throughout the whole industry chain. In this context, critical technologies and available flexible resources at different levels of IESs, i.e., the transmission, distribution/district, and residential levels, are reviewed first in this paper. Then, flexible resources in the source, network, load, and storage are remodeled to minimize carbon emissions more directly. In this manner, CO2 in the whole industry chains of IESs can be marked and traced, which is named after the “all-carbon chain” here. Besides, as an original content of this paper, new technologies, i.e., CO2 flooding and Organic Rankine Cycle (ORC), get introductions for low-carbonizing IESs further. Last but not least, an actual large-scale IES is employed to verify the proposed approach from the transmission and distribution/district levels. It is concluded that the all-carbon chain is complex-less when applied in a bi-layer integration process and a weak-convex update formula also could ensure convergence (within 44 iterations). Besides, our approach helps to cut carbon emissions when compared with the traditional IES (by 50.61%) and two low-carbon IESs (by 18.37% and 12.09%). Moreover, our method makes IES enjoy a purposeful evolution for more functions of low-carbonization, source tracing, targeted evolution, and contribution quantification are covered.