This study focuses on two types of phosphonium cation-based ionic liquids (P-ILs) with different alkyl chains: triethylalkylphosphonium (P222R) and tributylalkylphosphonium (P444R) cations. Broadband dielectric spectroscopy showed that the translational motion of the ions accelerated with an increasing number of alkyl chains by coupling with their rotational motion in both P-ILs. Raman spectroscopy revealed that P222R cations, despite dielectric similarities to P444R cations, can form all-trans conformations and cation-rich nanodomains because they have a relatively polar, short alkyl chain moiety with a central P atom and less-polar alkyl chains than those of P444R cations. Furthermore, the P222R cations had less effect on the conformational changes of the anions than those of P444R cations. These findings are supported by density functional theory calculations. Based on the results of terahertz spectroscopic analysis, these molecular structures originated from the different intermolecular interactions between the cations and anions.