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A highly sensitive optical fiber temperature sensor based on a section of liquid-filled silica capillary tube (SCT) between single mode fibers is proposed. Two micro-holes are drilled on two sides of SCT directly by using femtosecond laser micromachining, and liquid polymer is filled into the SCT through the micro-holes without any air bubbles and then sealed by using ultra-violet (UV) cure adhesive. The sidewall of the SCT forms a Fabry–Perot resonator, and loss peaks are achieved in the transmission spectrum of the SCT at the resonant wavelength. The resonance condition can be influenced by the refractive index variation of the liquid polymer filled in SCT, which is sensitive to temperature due to its high thermo-optical coefficient (−2.98 × 10−4 °C−1). The experimental result shows that the temperature sensitivity of the proposed fiber structure reaches 5.09 nm/°C with a perfect linearity of 99.8%. In addition, it exhibits good repeatability and reliability in temperature sensing application.