Fish collagen, derived from sustainable sources, offers a valuable substrate for generating peptides with diverse biofunctionalities. In this study, alkaline, papain, and ginger protease were used to enzymatically hydrolyze fish skin collagen. The peptide molecular weight distribution and sequence were measured using HPLC and ICP-MS-MS, with papain/alkaline protease (AP) and papain/alkaline/ginger protease (APG) hydrolyzed samples compared. As the results showed, the incorporation of ginger protease was useful for increasing the degree of hydrolysis, with the content of <400 Da peptides increasing from 49.82% to 58.56%. The identified peptide sequence in the APG sample had more proline at the C-terminal. The peptides were separated into two components (different in molecular weight) using gel column chromatography. The molecular weight distribution, amino acid composition, ACE inhibitory activity, and fibroblast proliferation activity of the collected components were measured. In comparison, the contents of proline and hydroxyproline in the larger peptides decreased obviously after combined hydrolysis by ginger protease, reflecting the formation of a peptide sequence of smaller molecular weight containing glycine and hydroxyproline. The combined hydrolysis of ginger protease was beneficial for the improvement of the ACE inhibitory activity of the sample. However, the fibroblast proliferation activity of AP was higher than that of APG, indicating that further hydrolysis by ginger protease may destroy the hydroxyproline at the end of the peptide sequence. This study proposed a creative directional hydrolysis method and provided practical guidance for the production of collagen peptides with enhanced functional activity.