The well-ordered assembly of collagen molecules on mica surface has attracted extensive attention because it has great potential applications or can be served as a model system for study on the assembly process. Although the epitaxially guided collagen assembly mediated by potassium ion on mica surface has been reported several times over these years, specific effects of anions in this field has never been surveyed and discussed before now. In this work, atomic force microscopy was employed to visually follow the assembly of collagen on mica surface mediated by three kinds of Mg2+ salts with different anions, including MgAc2, MgSO4, and MgCl2. It was found that at high ionic concentration anions could critically affect the interaction between collagen microfibrils and mica surface and accordingly resulted in different structures. Almost parallelly aligned collagen fibrils in one direction were achieved for acetates, sparse and small fibrils in two main directions rotated by 120 degrees were acquired for sulfate, while flat film with some defects was obtained for chloride, respectively. The Hofmeister series and Collins' model were used to interpret the results. This study would be useful for controlling the morphologies of assembled collagen on a surface.