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When using magnetic resonance sounding (MRS) method for groundwater, the detection accuracy is often affected by electromagnetic noise. The chaos method can achieve signal extraction at a lower signal-to-noise ratio. However, this method has many problems when used to obtain MRS signals. Aiming at the attenuation characteristics of MRS signals, in this paper we propose a pre-segmentation method of MRS signals to improve the accuracy of chaos detection. In addition, a chaotic detection system model suitable for MRS signal recognition was constructed, and a calculation method for center-covered was used to improve the efficiency of determining the chaotic state. Through a large amount of simulation data, we have verified that this method can reliably extract MRS signals with a signal-to-noise ratio (SNR) of -30 dB, which provides technical support for the MRS method to work with a relatively high electromagnetic noise.