The invention provides a melt direct writing process based micro-channel chip manufacturing processing system. The system comprises a melt direct writing deposition device, a curing agent liquid adding device and a control device. The control device comprises a microprocessor, the melt direct writing deposition device comprises a heating module, an injector, a metal needle, a motion platform, a collection plate and a high-voltage power source. The injector comprises a liquid storage chamber which is internally provided with a polymer material, the lower end of the liquid storage chamber is connected with the metal needle while the upper end is connected with a pneumatic pump, and the pneumatic pump is connected with the microprocessor. The heating module is arranged on the outer side of the liquid storage chamber, the metal needle is arranged above the collection plate, a plane of the metal needle is perpendicularly intersected with a plane of the collection plate, the metal needle isconnected with a high-voltage output terminal of the high-voltage power source, and the collection plate has a zero potential. By means of melt direct writing for manufacturing a micro-channel main mould, the main mould width is reduced, the main mould depth is increased, and a depth-to-width ratio of a micro-channel chip after copying and curing of a curing agent is increased.