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Nano-volt magnetic resonance sounding (MRS) signals are sufficiently weak so that during the actual measurement, they are affected by environmental electromagnetic noise, leading to inaccuracy of the extracted characteristic parameters and hindering effective inverse interpretation. Considering the complexity and non-homogeneous spatial distribution of environmental noise and based on the theory of adaptive noise cancellation, a model system for noise cancellation using multi-reference coils was constructed to receive MRS signals. The feasibility of this system with theoretical calculation and experiments was analyzed and a modified sigmoid variable step size least mean square (SVSLMS) algorithm for noise cancellation was presented. The simulation results show that, the multi-reference coil method performs better than the single one on both signal-to-noise ratio (SNR) improvement and signal waveform optimization after filtering, under the condition of different noise correlations in the reference coils and primary detecting coils and different SNRs. In particular, when the noise correlation is poor and the SNR<0, the SNR can be improved by more than 8 dB after filtering with multi-reference coils. And the average fitting errors for initial amplitude and relaxation time are within 5%. Compared with the normalized least mean square (NLMS) algorithm and multichannel Wiener filter and processing field test data, the effectiveness of the proposed method is verified.