High energy density is always a key goal in the development of energy storage or energetic materials (EMs). Apart from exploring novel EMs with high chemical energy, it is also desirable for traditional EMs to be assembled at a higher density. It has been shown that a molecular level compression effect occurs due to the stacking of 2D triaminoguanidine–glyoxal polymer (TAGP) layers, resulting in a higher density packing of HMX molecules with changed conformation (qy-HMX). The qy-HMX crystal formed under compression in the solvent has a unit cell parameter very close to that of a reported system observed under a pressure of 0.2 GPa. This shows that the qy-HMX molecules are trapped in the TAGP layers, resulting in a higher density (e.g. 2.13 g cm⁻³), heat of formation and better stability. Certain types of constrained qy-HMX crystals are free from defects, where no polymorphic transition and melting point are observed upon heating. Experiments and relevant calculations show that the best resulted hybrid HMX crystal has a detonation velocity of 10.40 km s⁻¹ and pressure of 53.9 GPa, respectively. Its ground specific impulse reaches about 292 s, much better than that of CL-20, making it a promising propellant component for use in future space explorations.