In this study, we propose and analyze a temperature sensor based on whispering gallery modes (WGMs) in a cylindrical microresonator formed by metal-filled side-hole photonic crystal fiber (mSH-PCF). WGMs in the mSH-PCF microresonator are excited by evanescent light coupling using a tapered single-mode silica fiber. The application of temperature to the mSH-PCF microresonator causes a change in both the geometric shape of the microresonator and the refractive index produced by the thermal expansion of the filler metal, resulting in a linear shift of the WGM resonances in which the WGM quality factors do not decrease significantly during temperature changes. We also demonstrate that the temperature sensitivity of this platform is governed by the interaction between the microresonator and the fiber taper. Bismuth and indium were used to examine the effect of metal composition on temperature sensitivity. The measurements show that a maximum temperature sensitivity of 18.72 pm/°C can be achieved with the indium-filled PCF. The experimental results are in good agreement with the numerical simulations. WGM shifts were found to depend mainly on cavity deformation.