Estimations of the surface soil moisture and distributions play a key role in the ecological, environmental, and topographical investigations for intertidal mudflats that are characteristically wet and periodically submerged by sea water. However, existing techniques have limitations of measurement. Along with the three-dimensional (3D) point cloud, long-range terrestrial laser scanners (TLSs) can simultaneously record the co-located intensity value of each echo that internally contains physical reflectance characteristics of the scanned point. Most long-range TLSs emit near-infrared lasers that can be strongly absorbed by the water. Thus, the intensity values of the areas with high water moisture are theoretically smaller than those of the regions with low moisture. In this study, the intensity data of long-range TLSs are corrected for the incidence angle and distance effects and the corrected intensity data are utilized to quantitatively estimate the surface soil moisture of intertidal mudflats. A case study is conducted for a mudflat in Chongming Island, Shanghai, China, using a long-range TLS (Riegl VZ-4000) that can measure distance up to 4000 m with a near-infrared wavelength of 1550 nm. Results show that compared with traditional techniques (e.g., gravimetric measurements) the corrected intensity data of long-range TLSs are a very effective data source for a quick, accurate, and detailed estimation of surface soil moisture for large-area mudflats. The estimation accuracy is approximately 97%. Additionally, by combining the point cloud of the mudflats the 3D distribution of the moisture can be accurately mapped to potentially analyze the intrinsic association between moisture and topography, vegetation coverage, and habitation of creatures in mudflats.