An approach of using phase modulation spectroscopy (PMS) system has been proposed which has single frequency, dual-wavelength with phase-only output for oximetry to minimize the inflences of room light in the clinical environment. The availability of this method has been verified by Laboratory experiments both in vitro and in vivo. In this study, a 200Mhz PMS system has been used for measuring on piglet brain in vivo, to detect blood volume and saturation change during normoxia to hypoxia periods, and to monitor the brain depolarisation in the hypoxic stress. Our experimental results show that the brain saturation estimated by PMS is approximatedly 84% and lies between arterial and venous blood values of 97% and 80% in normoxia, and tends to move close to the venous side in hypoxia. In addition, the excessive hypoxic stress triggers the brain to be bio-energetic deficits and finally introduced the neural depolarisation, which can be effectively detected by recording the increment of tissue scattering.