Based on the high-resolution oceanic numerical model product of MITgcm with a resolution of (1/48)°, the geostrophic balanced motion and unbalanced wave motion are decomposed via the frequency-wavenumber spectrum analysis method to analyze the distribution of submesoscale characteristics and diagnose the main factors affecting their seasonal variations in the Agulhas current system. The results show that the submesoscale processes in the Agulhas current system have a significant seasonal distribution with strong features in winter but weak features in summer. The mixed layer baroclinic instability is the main reason affecting the submesoscale seasonal differences in the area. In addition, the geostrophic balanced motions are predominant in the submesoscale process in the regions with stronger eddy kinetic energy (EKE) and have no obvious seasonality. For the regions with weaker EKE, the balanced and unbalanced geostrophic motions show significant seasonality, where the local mixing layer shallowness is responsible for the increase of the unbalanced kinetic energy in summer. Our analysis helps to further clarify the characteristics of submesoscale seasonal variation and its primary factors in the Agulhas current system. The effective separation of geostrophic balanced and unbalanced motion enhances our understanding of energy transformation between multiscale processes in the ocean.