Due to the limitation of the satellite attitude measurement accuracy and the system servo control error of the payload scanning mechanism, an optimal use of Micro-Wave Radiation Imager (MWRI) observations requires high geolocation accuracy. In the operational system, the MWRI geolocation accuracy reaches 1 pixel, and there still exists room for improvement. In this article, we improve upon the coastline inflection point method (CIM) and propose to assign the accurate correspondence by employing a nonrigid point set registration method. First, the method identifies a set of latent variables to recognize outliers and then applies nonparametric geometric constraints to the correspondence as <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a priori</i> distribution. Second, the maximum <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a posteriori</i> (MAP) estimation is applied by the expectation–maximization (EM) algorithm to obtain correct inliers. The comparison with other methods demonstrates that the proposed method can provide more accurate estimation of geolocation bias. In addition, the pixel error and changes in spacecraft attitude with the long-term geolocation data in FY-3C MWRI before and after correction were analyzed during the period from April 1 to August 30, 2018. The results have shown that the geolocation errors are reduced from [0.50, 0.60] pixels to [0.20, 0.33] pixels in the along- and cross-track directions after the attitude correction. In addition, the reduction of the standard deviation shows that the geolocation quality of MWRI is improved.