We have performed Li and Na ion charge-discharge experiments of 9,10-phenanthrene quinone (PhQ) molecules encapsulated in single-walled carbon nanotubes (SWCNTs) with mean tube diameters of 1.5 and 2.5 nm at room temperature and also at low temperatures. The Na ion reversible capacity of PhQ encapsulated in the larger diameter SWCNTs, measured at a low temperature of 0 °C, remained as high as that measured at room temperature (RT), while the capacity of PhQ in the smaller diameter SWCNTs at 0 °C was about a half of that at RT. The diameter dependence of the capacity should be attributed to the difference in the interactions between the encapsulated PhQ molecules and the host SWCNTs, which was revealed by Raman peak profile analysis. Charge-transfer reaction from metallic tubes to PhQ molecules encapsulated in the smaller diameter SWCNTs was detected by Raman measurements. The electrostatic interaction between charged SWCNTs and PhQ molecules, induced by the charge-transfer reaction, would partly contribute to the stabilization of PhQ molecules in the smaller diameter SWCNTs, while only van der Waals interaction stabilizes PhQ molecules in the larger diameter SWCNTs. The difference in stability was confirmed by thermogravimetric, x-ray photoelectron spectroscopy, and Raman measurements. Charge-discharge curves of PhQ encapsulated in SWCNTs were also discussed based on the stability difference.