A three-dimensional (3-D) printing apparatus and an inkjet coloring method thereof are provided. The 3-D printing apparatus includes a platform, a three-dimensional printing head, an inkjet head and the method includes following steps. A layer thickness of at least one layer object forming a 3-D object is obtained. An ink discharge volume of an ink layer is adjusted according to the layer thickness, wherein the ink discharge volume is in positive correlation with the layer thickness. A building material is melted and printed out on the platform according to the layer thickness by the three-dimensional printing head to form the at last one layer object. Ink is dispensed on the at last one layer object according to the adjusted ink discharge volume by the inkjet head to form the ink layer.