The application of salt-in-ionic liquid electrolytes (SILEs) in lithium-ion batteries is restricted by the negative transference number of lithium ion (tLi+) from strong ion-ion correlations. In this study, we applied molecular dynamics (MD) simulations on three imidazolium-based functionalized SILEs, composed of 1-hexyl-3-methylimidazolium (HMIM+), 1-(2-methoxyethoxy)methyl-3-methylimidazolium (MOEOMMIM+), or 1-[2-(methoxycarbonyloxy)ethyl]-3-methylimidazolium (EMCMIM+), and bis(trifluoromethanesulfonyl)imide (TFSI−), doped with 0.25 molar fraction of LiTFSI. MD simulations show that tLi+ is improved in the SILE composed of [EMCMIMTFSI]0.75[LiTFSI]0.25. Detailed analyses show that Li+ can coordinate with the carbonyl oxygen on the side chain of EMCMIM+, which competes with TFSI−, and thus weakens Li+–TFSI− coordination. On the other hand, one of ether oxygens on the side chain of MOEOMMIM+ tends to form intra-ionic hydrogen bonds (HBs) with the hydrogen atoms on the imidazolium ring, which even hinders the coordination between MOEOMMIM+ and TFSI−, and thus reinforces Li+–TFSI− coordination. The net result is that tLi+ increases in the order [MOEOMMIM] < [HMIM] < [EMCMIM]. These findings may help on the further design of functionalized SILEs toward a desired tLi+.