In this work, the SO3H-functionalized ionic liquids (SFILs) ([C(n)PSIm][HSO4], n = 1, 2, 4, 6, and 8) were investigated as cocatalyst mixed with the concentrated H2SO4 for the isobutane alkylation. The SFILs with longer alkyl chain show a better catalytic performance with the C8 selectivity up to 75.73 and RON up to 95.66, respectively. The better catalytic performance can be attributed to the better dispersion of isobutane in the SFIL/H2SO4 system led by the SFILs with longer alkyl chain, which is further correlated with the nanostructured-aggregation feature of the longer alkyl chain confirmed by MD simulation. In addition, the reusability of SFIL/H2SO4 mixture can reach up to 22 runs, outclassing the pure H2SO4. The MD simulation, quantum chemistry calculations, and NMR spectra revealed that cationic clusters are formed by the strong hydrogen bonds between the sulfonic acid group and the H2SO4, which is beneficial to the longer lifetime of the SFIL/H2SO4 mixtures. Hopefully, the useful information in this work will provide valuable insights into the screening and design of novel SFILs for the H2SO4 alkylation.