An alignment method adopted by a 3D printer (1) having a 3D nozzle (111) for jetting material and a 2D pen-module (112) for jetting colored ink is disclosed. The 3D printer (1) first controls the 3D nozzle (111) to print an alignment template (2) on a printing platform (12), wherein the alignment template (2) comprises multiple alignment blocks (24) respectively and separately printed along an axis, and each alignment block (24) respectively deviates from each center-line (22) according to an accumulated offset. Next, the 3D printer (1) controls the 2D pen-module (112) to print an ink matrix (3) on the alignment template (2), wherein the ink matrix (3) comprises multiple ink blocks (31) respectively and separately printed along the same axis, and each ink block (31) is exactly corresponding to each center-line (23) respectively. The 3D printer (1) uses covering status of each alignment block (24) and each ink block (31) to determine a deviation between the 3D nozzle (111) and the 2D pen-module (112), so as to perform an alignment action thereupon.