The present invention belongs to the technical field of irrigation and water conservancy, and discloses a method for acquiring anisotropic basin surface roughness and use thereof. The method includes: preselecting two experimental strip fields respectively parallel to length direction and width direction of a target basin, to respectively acquire first surface water flow advancing process data of the two experimental strip fields, where the target basin may be regarded as a square-shaped field; acquiring two pieces of isotropic basin surface roughness respectively by using one-dimensional complete hydrodynamic model for basin irrigation according to the surface water flow advancing process data; and substituting the isotropic basin surface roughness into an elliptic equation that anisotropic basin surface roughness satisfies, to solve anisotropic basin surface roughness of the target basin, the anisotropic basin surface roughness including basin surface roughness components parallel to and perpendicular to shallow furrows on basin surface and crop planting direction in the target basin. The anisotropic basin surface roughness can truly reflect the resistance of the basin surface against the water flow, thereby improving simulation precision of surface irrigation hydrodynamics, and acquiring more accurate irrigation performance indexes.