Molecular perovskites are promising practicable energetic materials with easy access and outstanding performances. Herein, we reported the first comparative thermal research on energetic molecular perovskite structures of (C6H14N2)[NH4(ClO4)3], (C6H14N2)[Na(ClO4)3], and (C6H14ON2)[NH4(ClO4)3] through both calculation and experimental methods with different heating rates such as 2, 5, 10, and 20 °C/min. The peak temperature of thermal decompositions of (C6H14ON2)[NH4(ClO4)3] and (C6H14N2) [Na(ClO4)3] were 384 and 354 °C at the heating rate of 10 °C/min, which are lower than that of (C6H14N2)[NH4(ClO4)3] (401 °C). The choice of organic component with larger molecular volume, as well as the replacement of ammonium cation by alkali cation weakened the cubic cage skeletons; meanwhile, corresponding kinetic parameters were calculated with thermokinetics software. The synergistic catalysis thermal decomposition mechanisms of the molecular perovskites were also investigated based on condensed-phase thermolysis/Fourier-transform infrared spectroscopy method and DSC-TG-FTIR-MS quadruple technology at different temperatures.