Novel thienylcyanostyrene and pyridinium-based luminescent ionic liquid crystals (ILCs) characterized with different length of N-alkyl chains (N–C3H7 and N–C8H17) and different size of counter anions (Br−, BF4−, PF6− and Tf2N−) on pyridinium moiety have been synthesized. The chemical modifications of N-alkyl chains and counter anions are easily achieved via pyridine alkylation followed with further ion exchanges, which played a key role in tuning supramolecular self-assembly of these ILCs. The compounds with shorter N–C3 alkyl chain (E-CTPC3X, X = Br−, BF4−, PF6− and Tf2N−) can self-assemble into 3D cubic phase or 2D hexagonal columnar phase depending on the size of counter anion, while the analogues with longer N–C8 alkyl chain (E-CTPC8X, X = BF4− and Tf2N−) only result smectic A phases. Moreover, the prolongation of the N-alkyl chain or enlargement of counter anion could significantly decrease the clear points of LC phases avoiding the thermal decomposition at high temperature, whereas introducing counter anions such as BF4−, PF6− that can form hydrogen bonds have stabilized the LC phases. The notable negative fluorosolvatochromism and the photoinduced fluorescence conversion with high-contrast of these ILCs were observed using UV–vis absorption and photoluminescence (PL) spectra, and was further analyzed by dynamic 1H NMR. These ILCs had been used as dopant to modify the n-Si/PEDOT:PSS heterojunction solar cells (HSCs) with 2 fold hole mobility (μhole) enhancement of the PEDOT:PSS layer.