Objective. To prepare biocompatible ciprofloxacin-loaded carboxymethyl chitosan nanoparticles (CCC NPs) and evaluate their cell specificity as well as antibacterial activity against Escherichia coli in vitro. Methods. CCC NPs were prepared by ionic cross-linking method and optimized by using Box-Behnken response surface method (BBRSM). Zeta potential, drug encapsulation, and release of the obtained nanoparticles in vitro were thoroughly investigated. Minimum inhibitory concentration (MIC) and killing profiles of free or ciprofloxacin-loaded nanoparticles against Escherichia coli were documented. The cytotoicity of blank nanoparticles and cellular uptake of CCC NPs were also investigated. Results. The obtained particles were monodisperse nanospheres with an average hydrated diameter of 151 ± 5.67 nm and surface of charge −22.9 ± 2.21 mV. The MICs of free ciprofloxacin and CCC NPs were 0.16 and 0.08 μg/mL, respectively. Blank nanoparticles showed no obvious cell inhibition within 24 h, and noticeable phagocytosis effect was observed in the presence of CCC NPs. Conclusion. This study shows that CCC NPs have stronger antibacterial activity against Escherichia coli than the free ciprofloxacin because they can easily be uptaken by cells. The obtained CCC NPs have promising prospect in drug delivery field.