The development of integrated microfluidic systems/platforms concerns many fields. Current remarkable integrated systems based on stacking multi-layer polydimethylsiloxane (PDMS) require complicated fabrication and operation and still remain challenging. We propose a novel micro-millifluidic processing system (MPS) comprising three core modules: a motherboard, a control panel and microfluidic chips. Fluids are handled in sub-millichannels in a motherboard and functional operations occur in microchannels in microfluidic chips. A motherboard with versatile functional units for fluid handling was monolithically fabricated via multimaterial 3D printing, which avoids multi-layer structures, and the major disadvantage of current 3D printing, i.e. low resolution, has been overcome by integrating novel microfluidic chips based on our developed maskless lithography platform. Both numerical and experimental studies were conducted to validate our system. Potential applications such as droplet generation and distribution, microfluidic mixing and simple bacterial resistance tests have been demonstrated via our MPS.