The transition from Landsat Collection 1 to Collection 2 introduced significant improvements in radiometric and geometric accuracy. However, the improvements cause location misalignment between the existing Landsat-derived land cover products and the new collection. The legacy National Land Cover Database (NLCD) has been used as a cornerstone land cover source for a variety of research. Therefore, a method aligning the legacy NLCD product to Collection 2 is required to ensure its continuity and consistency of service. We developed a strategy to not only align legacy NLCD to match new Collection 2 geometric locations but also improve land cover labeling in the region that was affected by the geometric shifts. The method identifies boundary pixels of homogeneous land cover patches as potential problem areas that are likely impacted by geometric shifts and generates candidate labels from 3 × 3 window with the target pixel at the center and segmentation-derived majority label. Standard phenology patterns of each candidate land cover type are established based on the random samples except boundary pixels within a 1000-pixels × 1000-pixels processing window region. The phenological distance to each standard land cover type pattern is calculated through a penalty dynamic time warping (DTW) method for each target pixel in the boundary region. Finally, the method determines the most suitable label based on the phenological distance from the candidate labels. Both visual and accuracy assessment results demonstrate that the alignment preserves the overall land cover patterns in the original legacy NLCD product while reducing the spatial discrepancies between the Landsat Collection 2 and land cover. In addition, it enhances the accuracy of land cover labeling of boundary pixels. The overall accuracy (OA) was increased by 7% in the land cover boundary regions after alignment. The quality and confusion matrix comparison between the alignment results and the original legacy NLCD confirm the reliability of the method. Our alignment method has the potential to serve as a framework for aligning other Landsat-derived land cover products to future collections.