The controlled synthesis of functional nanoparticles with tunable structures and properties has been extensively investigated for cancer treatment and diagnosis. Among a variety of methods for fabrication of nanoparticles, microfluidics-based synthesis enables enhanced mixing and precise fluidic modulation inside microchannels, thus allowing for the flow-mediated production of nanoparticles in a controllable manner. This review focuses on recent advances of using microfluidic devices for the synthesis of drug-loaded nanoparticles with specific characteristics (such as size, composite, surface modification, structure and rigidity) for enhanced cancer treatment and diagnosis as well as to investigate the bio-nanoparticle interaction. The discussion on microfluidics-based synthesis may shed light on the rational design of functional nanoparticles for cancer-related pharmaceutical applications.