An image alignment adjustment mechanism of a scanner and an adjustment tool for adjusting a scanning module (4) are provided. The image alignment adjustment mechanism includes a housing (10) and an adjustment device (2) arranged in the housing (10). The housing (10) has a guiding structure (13) for moving the scanning module (4). The adjustment device (2) includes a base (20), a connection portion (21) extending from the base (20), and an adjustment portion (22). An adjustment area (102) is defined on the housing (10) corresponding to the adjustment device (2), an adjustment hole (103) is defined on the housing (10) corresponding to the adjustment area (103), and the base (20) is arranged in the housing (10) adjacent to the adjustment area (102). The connection portion (21) is coupled to the guiding structure (13), and the adjustment portion (22) protrudes from the adjustment hole (103).