In condensed matter, phase separation is strongly related to ferroelasticity, ferroelectricity, ferromagnetism, electron correlation, and crystallography. These ferroics are important for nanoelectronic devices such as non-volatile memory. However, the quantitative information regarding the lattice (atomic) structure at the border of phase separation is unclear in many cases. Thus, to design electronic devices on the molecular level, a quantitative relationship must be established between the lattice and the electrons. Herein, we elucidated a Pd II -Pd IV /Pd III -Pd III phase transition and phase separation mechanism for [Pd(cptn) 2 Br]Br 2 (cptn = 1R,2R-diaminocyclopentane), propagated through a hydrogen-bonding network. Although the Pd•••Pd distance was used to determine the electronic state, the differences in the Pd•••Pd distance and the optical gap between Mott-Hubbard (MH) and charge-densitywave (CDW) states were only 0.012 Å and 0.17 eV, respectively. The N-H•••Br•••H-N hydrogen-bonding network functioned as a jack, adjusting the structural difference dynamically, and allowing visible ferroelastic phase transition/separation in a uctuating N 2 gas ow. In addition, the effect of the phase separation on the spin susceptibility and electrical conductivity were clari ed to represent the quasiepitaxial crystals among CDW-MH states. These results indicate that the phase transitions and separations could be controlled via modi cations at the atomic and molecular levels, such as the addition of hydrogen bonding.