A method for measuring blood oxygen content under low perfusion, which is used in a device for measuring blood oxygen content, includes the steps of: initializing the device that is applied with power, collecting and processing data with a driving circuit of light emitting device, a bias circuit, a gain circuit and an A/D sampling circuit, which are controlled under a core control module; calculating blood oxygen saturation based on the collected data with a data processing module which integrates the collected data in a period of time with an area integration method; and outputting from a communication functional module results of the blood oxygen saturation or pulse rate calculated with the data processing module. The method further includes a decision step of deciding the two results acquired from the data processing module with the waveform method and the integration method respectively based on the intensity of the measured signal and generating the final measured result, performed by a decision unit included in the device. By adopting the above method, the disturbance to effective signal by noise can be eliminated. As a result, the measuring accuracy of blood oxygen content under low perfusion can be improved without increasing the production cost for the measuring device.