Fluorodinitromethyl (FDN, CF(NO2)2) is a crucial substituent for energetic materials (EMs), known for its superior thermal stability compared to other polynitro groups. However, some research contradicts this conclusion. To gain deeper insights into the relationship between substituent effects and thermal and storage stabilities, we investigated five series of EMs with different polynitro group substitution patterns. In addition to FDN, nitroform (C(NO2)3), gem-dinitro (CH(NO2)2), and gem-dinitro anion (C(NO2)2−) groups were investigated. Bond dissociation energy (BDE), aromaticity, localized orbital locator (LOL), and electrostatic potentials (ESPs) were studied for 20 EM compounds. BDE analysis revealed that the rate-determining step in the thermal decomposition is polynitro C-NO2 bond cleavage except for b serie. C(NO2)2− conferred the highest BDE followed by FDN. Aromaticity analysis revealed minimal differences in ICSS values within a compound series, so the influence of aromaticity on thermal stability can be disregarded. Electron localization within the rings was consistently higher for CH(NO2)2 and C(NO2)3 than FDN and C(NO2)2− indicating that the latter possesses greater thermal stability, consistent with BDE analysis. ESP analysis revealed that C(NO2)3 conferred the lowest reactivity and the highest storage stability followed by FDN.