Ionic liquids (ILs) are promising materials for enhancing the electrical conductivity and stretchability of poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)‐based stretchable transparent conductors. However, the relationship between the chemical structures of ILs and the electrical and mechanical properties of PEDOT:PSS/IL composites remains unclear. In this study, the impact of protic ILs (p‐ILs) on the electrical conductivity and stretchability of PEDOT:PSS/IL thin films is investigated via a comparative analysis with aprotic ILs (ap‐ILs). By synthesizing a series of p‐ILs and ap‐ILs based on imidazolium (IM) and bis(trifluoromethanesulfonyl)imide ions, it is demonstrated that p‐ILs significantly enhance electrical conductivity and stretchability, outperforming ap‐ILs. In addition, these properties further improve with decreasing alkyl chain length of IM cations, achieving maximum electrical conductivity and stretchability of ≈2200 S cm−1 and 65%, respectively. Notably, the crystalline structures of PEDOT:PSS/IL thin films are elucidated, revealing that p‐ILs with shorter alkyl chains facilitate the formation of PSS crystallites due to hydrogen bonding between p‐ILs and PSS, which in turn enhance electrical conductivity and stretchability. Leveraging these insights, PEDOT:PSS/p‐IL‐based strain sensors with broad dynamic ranges and tunable gauge factors are developed. The findings of this study provide valuable design guidelines for developing high‐performance ILs in stretchable and wearable electronics.