The invention provides a method for eliminating a direct coupling signal of a sensing logging instrument and a device thereof. A transmitting unit of the device comprises a transmitting coil; a receiving unit comprises a receiving coil, a compensating coil, a phase comparator and an amplitude measuring circuit, wherein, the input signals of the phase comparator are respectively a current or voltage signal passing through the transmitting coil and the sensing voltage of the receiving coil and used for measuring the sensing voltage of the receiving coil and the phase difference of the current or voltage signal passing through the transmitting coil under the following two conditions: the portion of the direct coupling signal of the sensing voltage of the receiving coil is increased in the air until a secondary sensing signal is small enough relative to the direct coupling signal, and the phase difference Theta 1 is measured; under normal condition, the phase difference Theta 2 is measured; the amplitude measuring circuit is used for measuring the amplitude value A of the sensing voltage of the receiving coil in a stratum under normal condition; and the formulas that R equals to A multiplied by sin (Theta 3) and Theta 3 equals to Theta 2 minus Theta 1 are utilized to calculate the amplitude value of the secondary sensing voltage. The method and the device can eliminate the errors caused by the phase displacement of the instrument and effectively eliminate the direct coupling signal.