This paper introduces an innovative nanotechnology-based approach that provides a pathway to enhance the energy release efficiency of nanoenergetic materials (nEMs) by harnessing self-synchronized collective atomic vibrations and phonon wave resonance within the transition domains between nanocomponents, without altering the material composition. The key innovation involves incorporating finely-tuned 2D-ordered linear-chain carbon-based multilayer nano-enhanced interfaces as programmable nanodevices into the transition domains using advanced multistage processing and assembly techniques. These programmable nanodevices enable precise control over self-synchronized collective atomic vibrations and phonon wave propagation, leading to synergistic effects. To activate and optimize these effects, a combination of various methods is employed, including energy-driven initiation of allotropic phase transformations, surface acoustic wave-assisted micro/nano-manipulation, heteroatom doping, directed self-assembly using high-frequency electromagnetic fields, and data-driven inverse design approaches. By leveraging a data-driven inverse design strategy and uncovering hidden structure-property relationships, we maximize energy release efficiency using the carbon nano-materials genome approach derived from multifactorial neural network-based predictive models. This approach not only unlocks new functionalities in nEMs but also improves environmental performance and safety levels. By pioneering transformative pathways for nEMs through harnessing phonon wave resonance in low-dimensional nanocarbon transition interfaces, this research brings significant advancements in the field.