The effect of the chain length of the alkyl and alkoxy substituents on the binding characteristics of 1-alkyl-6-alkoxy-quinolinium cations was studied using 4-sulfonatocalix[4]arene (SCX4) and 4-sulfonatocalix[6]arene (SCX6) in neutral aqueous solutions at 298 K. Isothermal calorimetric titrations showed enthalpy-controlled inclusion with 1:1 stoichiometry. The equilibrium constants of complexation were always larger for the confinement in SCX4 than in its SCX6 homologue because the better matching between the host and guest sizes allowed more exothermic interaction. The binding affinity diminished with the lengthening of the aliphatic chain of the guests in the case of the association with SCX4, but insignificant change was found for SCX6 complexes. The most substantial change in the enthalpic and entropic contributions to the driving force of complex production occurred when the alkyl chain was linked to the heterocyclic nitrogen and the number of its carbon atoms varied between 1 and 4. 1H NMR spectra evidenced that in SCX6, the 1-alkyl-6-alkoxy-quinolinium cations could be included within the macrocycle cavity. In the case of SCX4, the quinolinium ring is always inside the host, but the alkyl chain is included within SCX4 only for a short chain length (n up to 4). In contrast, the alkoxy chain displays a very weak interaction with the cavity irrespective of the length. Because of the outward orientation from the host, the lengthening of the alkoxy substituent of the quinolinium moiety barely influenced the thermodynamics of inclusion in SCX4. Distinct linear enthalpy-entropy correlations were found for the encapsulation in SCX4 and SCX6.