With the development of science and technology, nuclear magnetic resonance (NMR) phenomenon has been studied. It has already entered the stage of application and development by theoretical research and test. In addition, it has also been widely used in geoscience (proton magnetometer, NMR spectrometer, core testing instrument and NMR logging). On the basis of this, the NMR technique is proposed to detect the numerical simulation of groundwater. The simulation model of layered earth aquifer is established. The simulation results show that the water content of the aquifer, the change of the area of the coil and the depth of the aquifer all have some influence on the NMR signal. That is, the same NMR signal tested on the ground may be the response of the aquifer with the same depth, different thickness and water content on the ground. This also means that the measured data in one location in the field can be retrieved into the results of different stratigraphic models.