A novel fiber-optic thermometer based on a thick silicon Fabry-Pérot interferometer (FPI) realized on the tip of a cleaved single-mode fiber has been designed and implemented, in order to achieve high resolution and high sampling rate necessary for studying underwater turbulent microstructures. The choice of silicon for its large thermal-optic coefficient and thermal expansion coefficient enables a high sensitivity of 84 pm/°C. A new data processing method, using average wavelength tracking, is proposed to reduce the wavelength noise. The high sensitivity along with the low wavelength noise results in a temperature resolution as high as 0.0009 °C. Furthermore, the good thermal conductivity of silicon endows the proposed sensor with a response time ~ 2 ms, which allows a sampling frequency of 500 Hz. By further optimizing the sensor structure, e.g. size of the silicon FPI, a better temperature resolution and quicker response can be expected. This novel temperature sensor significantly augments underwater sensing capabilities, especially those related to microstructure turbulence mixing process in the ocean. A preliminary experimental demonstration is presented, where the sensor was used to measure the highly dynamic temperature variations induced by a sharp thermo-gradient underwater.