The invention relates to a method for eliminating noise of underground water detection signals based on near-end reference coil nuclear magnetic resonance. The method comprises the steps of simultaneously receiving data of 1 detection coil and n reference coils, and dividing data D acquired by a multi-channel nuclear magnetic resonance detector into data of a first half section and data of a second half section according to sampling time; carrying out discrete Fourier transform on the data of the first half section and the data of the second half section to obtain frequency domain data of thefirst half section and the second half section of the reference coils; calculating a transfer function H of the data of the second half section of the reference coils and detection coil in a frequencydomain; calculating the frequency domain data of noise estimation of the data of the first half section in the detection coil by using the transfer function H and the frequency domain data of the first half section of the reference coils, and performing inverse discrete Fourier transform to obtain time domain data of noise related to the data of the first half section in the detection coil; and finally, carrying out noise elimination to obtain a processing result. The method for eliminating noise of underground water detection signals based on near-end reference coil nuclear magnetic resonance, provided by the invention, realizes the effective elimination of the related noise in the detection coil under the condition of near-end reference, and simultaneously does not lose the useful MRS signals in the detection coil.