Single-molecule localization technology has been widely used in single-particle tracking and super-resolution imaging of biological samples, as it can bypass the diffraction limit of optical systems. Multi-channel single-molecule localization uses multiple imaging channels to simultaneously track different targets or perform multi-color super-resolution imaging, and can also improve the axial depth of single-particle tracking or achieve higher localization precision and density for super-resolution imaging. However, the difference between images in each channel can affect collaborative localization or quantitative analysis, so image registration is a key step in its image data preprocessing. Moreover, due to the high precision of single-molecule localization, its requirements for multi-channel image registration accuracy are also high. Existing technologies generally use control point-based registration methods and often use complicated and precise methods to obtain fiducial images for locating control point pairs to achieve high-precision image registration, which involves high sample or experimental equipment requirements and is difficult to directly extend to other systems. Therefore, developed in this work, is a high-precision image registration method that can directly use randomly distributed fluorescent beads as fiducial samples based on local nonlinear transformation and elimination of mismatched points. By monitoring and iteratively filtering control points in the process of feature matching and transformation model parameter estimation to eliminate control point pairs that are not accurately matched due to inaccurate or poor precision of single-molecule localization, the adverse effects on accurate acquisition and precise matching of control points when using randomly distributed fluorescent beads as fiducial samples are eliminated. At the same time, a second-order polynomial fitting based on local weighted mean is used for estimating the transformation model parameter to better adapt to the existence of local nonlinear deformation between different channels. The results show that using this method only requires three iterations to find and eliminate control point pairs that are not accurately located and matched, thereby achieving more accurate transformation model parameter and improving the registration accuracy by an order of magnitude, achieving a registration accuracy of about 6 nm in a complex dual-channel single-molecule localization imaging system based on orthogonal astigmatism.