Owing to their central roles in cellular signaling, construction, and biochemistry, collagen-collagen interactions, and collagen self-assembly have become a major focus of molecular design and synthetic biology. The well-ordered assembly of collagen molecules on mica has attracted extensive attention for its essential applications and studies on the self-assembly process as a model system. Although collagen assembly mediated by various ions on mica has been reported over these years, specific effects of transition metal ions in this field have never been deeply surveyed and discussed till now. In this work, type I collagen extracted from rat tail tendon by pepsin solubilization method was selected to explore the kinetic process and self-assembly characteristics. In the presence of Cu2+ and Zn2+ sulfates, the turbidity method was used to directly measure the kinetic process of collagen self-assembly and atomic force microscopy (AFM) was applied to observe the patterns of collagen self-assembly on mica. The results showed that the favorable properties of transition metal coordination (bonding strength, directionality, and reversibility) were helpful for increasing the collagen fibrillogenesis rate, and at different ion concentrations, Cu2+ and Zn2+ ions affected the interactions between collagen molecules and mica surface by destroying the hydration membranes on the surface of collagen molecules and the hydrogen bonds between the amino acid residues of collagen molecules. Circular dichroism (CD) analysis demonstrated that collagen had complete triple-strand conformation in the presence of Cu2+ and Zn2+. These results and analysis would be helpful for directing the patterns of collagen self-assembly on a solid surface and provide theoretical guidance for creating collagen-based high-performance materials and/or adding functionality in materials for various applications.