The surface nuclear magnetic resonance (SNMR) technique exploits the NMR phenomenon to quantitatively determine the subsurface distribution of water. In the SNMR sounding system, deeper regions are probed by increasing the pulse moment (the product of the current amplitude and pulse duration). However, the amplitude of the current in the transmitter coil inevitably decays due to the energy loss in the storage capacitor. In practical application, the maximum amplitude of the current in one transmission process is recorded and used as the current amplitude. However, this approach results in errors in calculating the pulse moment and the sensitivity kernel function. In this paper, we build a simulation of the transmission process and the current decay phenomenon appears. From the simulation results, the current amplitude at the end of the pulse is 83% of the maximum. We present a dynamic duty cycle control strategy for a constant excitation current. We calculate the 1D sensitivity kernel function based on the two cases of constant and decaying excitation current, respectively. We observe that the maximum difference between them is greater than 200 nV/m. The inversion results based on a 1D aquifer model containing two aquifers show that the decaying excitation current results in aquifers deeper than the model and the water content of the second aquifer is 50% of the model. A comparative experiment between the decaying excitation current system and the constant excitation current system was conducted in a field experiment. Compared with traditional SNMR instruments, our new system can effectively avoid the phenomenon of excitation current decay in field experiments, and the new SNMR sounding system enables accurate inversion of aquifers.