In the present study, the effectiveness of paclitaxel nanocrystals (PTX NCs) encapsulated in carboxymethyl chitosan (CMCS) nanoparticles (CMCS−PTX NPs) as an anticancer drug is evaluated. The CMCS nanoparticles are produced via a cross‐junction microfluidic device where the PTX/CMCS concentration and flow rates in the device are optimized. The dynamic light scattering data show that the PTX NCs have a median diameter size of 230±90 nm, while the size of CMCS−PTX NPs is roughly 270±30 nm. The zeta‐potential result indicates less negative surface charge for the CMCS−PTX NPs as compared to the PTX NCs. Moreover, scanning electron microscopy micrographs, differential scanning calorimetry thermograms, and X‐ray diffraction patterns reveal that the physicochemical properties of the drug remain unaltered after perfusion through the microfluidic device. Cytotoxicity and cell endocytosis of PTX NCs and CMCS−PTX NPs are evaluated in vitro using G361 melanoma‐positive skin cells. The results reveal that the CMCS−PTX NPs increase the cellular uptake and cytotoxicity compared to the PTX NCs alone. In addition, the antitumor effect of CMCS−PTX NPs on B16 melanoma indicates the great potential of CMCS as a promising nano‐carrier for PTX NCs drug with potent inhibitory effect on the tumor growth.