Layered packing structures have been of great interest in the field of energetic materials (EMs) due to their excellent balances between energy and safety. Nevertheless, the present advanced layered EMs and rational design approaches are still lacking. In this work, we proposed a multi-level structural design strategy for layered EMs, from molecular to crystal level. Inspired by the experimentally known energetic crystals with the specific NH2···NO2 intermolecular motifs, we established a set of guidelines for designing and screening potential target molecules based on the H2N–C–C–NO2 moiety via a systematic analysis of structure/composition–performance relationships. Subsequently, the possible crystal packing structures were searched accurately by the evolutionary algorithm USPEX coupled with a recently developed energetic molecule-specific polarizable force field. The theoretical results show that B1 (4,4′-diamino-3,3′-dinitro-[5,5′-biisoxazole] 2,2′-dioxide) and C2 [(E)-3,3′-(diazene-1,2-diyl) bis (4-amino-5-nitroisoxazole 2-oxide)] are promising candidates of advanced layered EMs with good mechanical sensitivities (better than TNT) and detonation performances (superior to FOX-7). Hopefully, our multi-level design procedure can accelerate the discovery of novel layered EMs with advanced properties.