The inhibition of clay surface hydration is a major hindrance for the use of water-based drilling fluids (WBDFs) in shale formations. In this work, a low molecular weight branched polyamine (BEN-5NH(2)) was synthesized and evaluated as a clay swelling inhibitor. The inhibition performance and rheological properties of the drilling fluids with BEN-5NH(2) were investigated by a linear swelling test, hot-rolling recovery test, and theological property test. The experimental results showed that BEN-5NH(2) exhibited better inhibition performance than that of the other inhibitors. Moreover, BEN-SNH 2 can balance the contradiction between the inhibition performance and rheological properties of the WBDFs. The inhibition mechanism of BEN-5NH(2) was investigated by X-ray diffraction, thermogravimetric analysis, scanning electron microscopy, X-ray photoelectron spectroscopy analysis, and density functional theory calculations. Based on the results, it was determined that BEN-5NH(2) can enter the interlayer space of sodium montmorillonite (Na-Mt), minimize the d-spacing of Na-Mt, and maintain the d-spacing of Na-Mt with the increase in relative humidity value. BEN-5NH(2) can replace the exchanged cations in the interlayer space of Na-Mt, remove the interlayer water, and thus completely inhibit interlayer surface hydration (zero-layer hydrate). The density functional theory simulation results showed that BEN-5NH(2) can be strongly adsorbed on the active site of Na-Mt (001) surface through electrostatic interaction and lie flat on the Na-Mt (001) surface. Therefore, BEN-5NH(2) is a promising clay swelling inhibitor with broad application prospects in water-based drilling fluids.