Commercialization of anion exchange membrane fuel cells (AEMFCs) has been limited due to the chemical degradation of various quaternary ammonium (QA) head groups, which affects the transportation of hydroxide () ions in AEMs. Understanding how various QA head groups bind and interact with hydroxide ions at the molecular level is of fundamental importance to developing high-performance AEMs. In this work, the binding and degradation reaction of hydroxide ions with several QA head groups—(a) pyridinium, (b) 1,4-diazabicyclo [2.2.2] octane (DABCO), (c) benzyltrimethylammonium (BTMA), (d) n-methyl piperidinium, (e) guanidium, and (f) trimethylhexylammonium (TMHA)—are investigated using the density functional theory (DFT) method. Results of binding energies (“∆” EBinding) show the following order of the binding strength of hydroxide ions with the six QA head groups: (a) > (c) > (f) > (d) > (e) > (b), suggesting that the group (b) has a high transportation rate of hydroxide ions via QA head groups of the AEM. This trend is in good agreement with the trend of ion exchange capacity from experimental data. Further analysis of the absolute values of the LUMO energies for the six QA head groups suggests the following order for chemical stability: (a) < (b)~(c) < (d) < (e) < (f). Considering the comprehensive studies of the nucleophilic substitution (SN2) degradation reactions for QA head groups (c) and (f), the chemical stability of QA (f) is found to be higher than that of QA (c), because the activation energy (“∆” EA) of QA (c) is lower than that of QA (f), while the reaction energies (“∆” ER) for QA (c) and QA (f) are similar at the different hydration levels (HLs). These results are also in line with the trends of LUMO energies and available chemical stability data found through experiments.