The pyramidal inversion of trisubstituted heteroatoms is well-recognized. However, the stereochemistry of bicoordinated heteroatoms is poorly developed and few examples assumedly isomerize by double-torsion motion or bond-angle inversion. Here, by using ab initio molecular dynamics combined with metadynamics simulation, we reveal an unexpected competing isomerization mechanism, namely dynamic π → σ* negative hyperconjugation induced coupled rotation of bond and bond angle leads to helix inversion in bis(trifluoromethane)sulfonamide (TFSI-), making TFSI- follow four distinct trans-cis isomerization pathways with diverse energy barriers (12–52 kJ mol-1) which are significantly higher than 3.6 kJ mol-1 of sole pathway estimated by conventional static calculations. Our quantitative simulations and experiments results confirm the positive correlation between overall stability of cis-TFSI- with polarity of countercations. The melting points (Tm) of TFSI--based ionic liquids (ILs) linearly rise with the conformational rigidity of TFSI- in the ion pair state, offering a new fundamental perspective on the origin of low Tm of ILs.