Structural regulation of magnetic nanomaterials has been pivotal for enhancing their magnetic properties and improving their performance in biomedical imaging. While numerous studies have focused on mesoscopic tuning of these nanocrystals, the desired level of precision has not been consistently achieved. The advent of atomic-level manipulation of nanostructures presents a sophisticated approach to the precise modulation of magnetism. However, a comprehensive understanding of how to modulate magnetism at the atomic level has remained elusive, impeding the advancement of this technique. This review aims to bridge this gap by conducting a thorough examination of the application of atomic-level techniques in magnetically modulating nanocrystals for biomedical imaging. It will synthesize current knowledge, elucidate the fundamental principles of atomic-level magnetic modulation, and highlight the contemporary biomedical imaging applications of these nanocrystals. The review will also discuss the challenges currently encountered and provide insights into emerging trends, suggesting potential directions for future research, thereby guiding the development of this rapidly evolving field.