The invention provides a phase comparison type differential protection method and system based on generator branch current. The method comprises the following steps: synchronously sampling the current of the branches of a generator; according to the sampling result, sequentially calculating the fault component of each phase branch current; according to the fault component of each phase branch current and with the Fourier filter algorithm, sequentially calculating the power frequency phasor of the fault component of each phase branch current; calculating the phase angle of the power frequency phasor of the fault component of each phase branch current in order; and conducting fault diagnosis to a large hydroelectric generator according to the phase angle of the power-frequency phasor of the fault component of each phase branch current. With the protection method and the system, it is possible to find the short circuit of different branches in the same phase across transition resistors as early as possible so as to reduce the loss of fault and ensure the a generator in fault to resume power supply in time.