A highly sensitive temperature sensor based on an all-fiber Sagnac loop interferometer combined with metal-filled side-hole photonic crystal fiber (PCF) is proposed and demonstrated. PCFs containing two side holes filled with metal offer a structure that can be modified to create a change in the birefringence of the fiber by the expansion of the filler metal. Bismuth and indium were used to examine the effect of filler metal on the temperature sensitivity of the fiber-optic temperature sensor. It was found from measurements that a very high temperature sensitivity of -9.0 nm/°C could be achieved with the indium-filled side-hole PCF. The experimental results are compared to numerical simulations with good agreement. It is shown that the high temperature sensitivity of the sensor is attributed to the fiber microstructure, which has a significant influence on the modulation of the birefringence caused by the expansion of the metal-filled holes.