SnSe is a topical thermoelectric material with a low thermal conductivity which is linked to its unique crystal structure. We use low-temperature heat capacity measurements to demonstrate the presence of two characteristic vibrational energy scales in SnSe with Debye temperatures D1 = 345(9) K and D2 = 154(2) K. These hard and soft substructures are quantitatively linked to the strong and weak Sn-Se bonds in the crystal structure. The heat capacity model predicts the temperature evolution of the unit cell volume, confirming that this two-substructure model captures the basic thermal properties. Comparison with phonon calculations reveals that the soft substructure is associated with the low energy phonon modes that are responsible for the thermal transport. This suggests that searching for materials containing highly divergent bond distances should be a fruitful route for discovering low thermal conductivity materials.