The output signal of fiber optic gyroscope (FOG) is a kind of nonlinear, nonstationary random signal. How to reconfigurate the signal is a problem for the output signal being filtered with empirical mode decomposition (EMD) filtering method, therefore the filtering method with EMD based on SNR testing is proposed in this paper. The filtered output signal is determined by testing continuously the enhanced grade of SNR between the two adjacent reconfiguration signal. The experimental results shows that this method can efficiently eliminate the noise in the output signal of FOG, and is an objective judgment means for the reconfigurating signal of EMD filtering method without any prior knowledge about noise in FOG.