A method for eliminating pump noise by empirical mode decomposition and particle swarm optimization is provided. In the method, based on a hypothesis of the pump noise being a linear combination of a group of bases, an extracted pump noise sample is decomposed into a group of signals as bases by the empirical mode decomposition. Coefficients of the optimized linear combination of the group of bases is determined by the particle swarm optimization, thus updating the pump noise sample and improving a noise elimination effect. During a limited number of noise elimination periods, a current pump noise sample is modified by weighting, such that in a limited number of iterations, the current pump noise sample gradually converges to the pump noise waveform in the unit of a varied period, so as to be applicable to a slow variation of the pump noise during a long-time operation of the system.
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