Micromotion refers to the small and non-uniform motion of the target or several target components along the radar line of sight. Using the high-resolution three-Dimensional (3D) Inverse Synthetic Aperture Radar (ISAR) imaging, the structural information and motion status of micromotion targets can be obtained, providing essential features for the detection, tracking, identification, and classification, which play important roles in the space situation awareness and ballistic missile defense. Given the complex micromotion forms and the non-stationary radar echoes, the available parametric ISAR imaging methods are no longer applicable. To overcome this limitation, this study aims to propose a high-resolution 3D imaging method for micromotion targets based on the scattering center trajectory matrix decomposition. First, the Range Instantaneous Doppler (RID) image series is generated to extract the support region of scattering centers by the watershed method. Then, the scattering center association is achieved based on the minimum Euclidean distance criterion. Considering the insufficient accuracy in the instantaneous slant range estimation with limited range resolution, a method for refined estimation of the trajectory matrix based on the modern spectrum analysis is proposed. Finally, the high-resolution 3D imaging of the micromotion targets is obtained by the trajectory matrix decomposition with constraints. The simulation results have demonstrated that the proposed method could effectively obtain high-resolution 3D imaging of the targets in complex micromotions such as nutation.