In this paper, a new method for synthesizing non-aqueous copper sulfide nanocrystals with different shapes and sizes using a homemade continuous-flow millifluidic chip is presented. Conventionally, the shape control of nanocrystals was accomplished using a surfactant-controlled approach, where directional growth is facilitated by selective passivation of a particular facet of the nanocrystals using surfactants. We demonstrate a "surfactant-free" approach where different sizes and shapes (i.e. spherical, triangular prism and rod) of plasmonic copper sulfide (Cu(2-x)S) nanocrystals can be fabricated by adjusting the flow rate and precursor concentrations. As continuous-flow synthesis enables uniform heating and easy variation of precursors' stoichiometries, it serves as an excellent incubation platform for nanoparticles due to its simplicity and high reproducibility. Transmission electron microscopy (TEM), fast Fourier transform (FFT) and X-ray diffraction (XRD) techniques were used to characterize the as-synthesized nanocrystals and revealed structures ranging from copper-deficient covellite (CuS), spionkopite (Cu1.39S), roxbyite (Cu1.75S), to copper-rich djurleite (Cu1.94S). The localized surface plasmon resonance (LSPR) peak of the nanocrystals can be tuned from 1115 to 1644 nm by simply varying the copper to sulfur molar ratio and flow rate. Furthermore, photothermal effects of Cu(2-x)S nanocrystals were also demonstrated to annihilate the RAW264.7 cells upon near infra-red laser irradiation.