The invention discloses a manufacture method for a three-dimensional micro-fluidic chip. The manufacture method comprises the following steps of: 1), casting a layer of liquid curable resin on a work surface, so as to form the bottom surface of the chip after curing; 2), spraying a runner solid material which can be dissolved to the solvent on the bottom surface of the chip to prepare a three-dimensional runner solid structure; 3), casting liquid curable resin on the three-dimensional runner solid structure, covering the three-dimensional runner solid structure, and curing to form the solid chip; 4), dissolving the three-dimensional runner solid structure in the solid chip by adopting solvent to acquire the three-dimensional micro-fluidic chip. The manufacture process is simple, the three-dimensional structure is precisely controllable and the manufacturing efficiency is high. The invention further discloses a three-axis machine tool which is improved on the basis of the conventional three-axis machine tool. A spindle shaft is changed to be a spray head, and the spray head is controlled by an XYZ-axis motion assembly of the three-axis machine tool to spray the runner solid material which can be dissolved to the solvent to form sections S1-Sn in sequences, so that a three-dimensional runner solid structure is acquired.