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Cu(tn)Cl2belongs to family of molecular magnets with low-dimensional magnetism mediated by hydrogen bonds. Here, the X-ray diffraction, electron paramagnetic resonance, specific heat measurements, and ab initio calculations performed within the framework of density functional theory have been employed to investigate the structural phase transition in Cu(tn)Cl2. Satellite reflections in the X-ray diffraction pattern from single crystals, visible anomaly in the specific heat measured in a zero magnetic field, rapid growth of the EPR resonance line width, along with the increase of the g-factors in the vicinity of 160 K are indicative of the structural phase transition in Cu(tn)Cl2. Our results reveal that this system undergoes transition from a disordered structure of the Pnmasymmetry to a modulated structure with the Pnma(0β0)s00 superspace group. The transition is reversible and driven by the reorientation of the diaminopropane ligands. The density functional theory studies support results of our specific heat measurements.