Fragmentations and ion-molecule reactions of ionized cyclohexane propionic acid and cyclohexane butyric acid were studied using FTMS and theoretical calculations. The difference in bond dissociation depending on the aliphatic chain length was investigated and mechanisms for the possible rearrangements depending on the aliphatic carbon length were suggested. The most abundant fragment ion of the ionized cyclohexane propionic acid was c-$C_6H_{11}CH_2;^+$ formed from the molecular ion by the direct C-C bond cleavage, while that of the ionized cyclohexane butyric acid was c-$C_6H_9C(OH)=OH^+$ formed by rearrangement of the molecular ion from the acid to diol form and loss of propyl radical. Stabilities of the radical and distonic ions of $C_nH_{2n}O^{+ullet}$ formed from the molecular ion were compared. Protonated molecules were dissociated into smaller ions by losing one or two water molecules. The $[nM + H]^+$, $[nM + H - H_2O]^+$, and $[nM + H - 2H_2O]^+$ with n = 2 and 3 were generated by solvation with the neutral molecules in the ICR cell at long ion trapping time.