Significant dynamic deformations during the operation of kilometer‐span high‐speed railway bridges adversely affect track maintenance. This paper proposes a three‐stage smoothness control method based on a comprehensive analysis of track alignment characteristics to address this issue. In the method, historical measured data are grouped into multicategories, and reference alignments for each category are reconstructed. Then, the reference alignment category to which the track to be adjusted belongs is accurately matched. Finally, a novel smoothness optimization algorithm is designed to use the 60 m chord as the optimization unit, and the 10 m and 30 m combined chords within the unit constrain the midchord offset and vector distance difference. The proposed method was applied to formulate the maintenance scheme for the Shanghai–Suzhou–Nantong Yangtze River Bridge. The result indicates that the track smoothness improved by more than 79.7%, and the high‐speed train operational performance improved by over 64.3%, effectively enhancing the maintenance quality.