By targeting CD44 receptors, inhibiting multidrug resistance (MDR), controlling drug release, and synergistically inhibiting tumor growth, a multilayered nanosystem was developed to serve as a multifunctional platform for the treatment of drug-resistant breast cancers. The multilayer nanosystem is composed of a poly(lactic-co-glycolic acid) core, a liposome second layer, and a chitosan third layer. The chitosan-multilayered nanoparticles (Ch-MLNPs) can co-deliver three chemotherapeutic agents: doxorubicin (DOX), paclitaxel (PTX), and silybin. The three drugs are released from the multilayered NPs in a controlled and sequential manner upon internalization and localization in the cellular endosomes. The presence of a chitosan layer allows the nanosystem to target a well-characterized MDR breast cancer biomarker, the CD44s receptor. In vitro cytotoxicity study showed that the nanosystem loaded with triple drugs, DOX–PTX–silybin, resulted in better antitumor efficacy than the single-drug or dual-drug nano-formulations. Likely attributed to the MDR-inhibition effect of silybin, the co-delivered DOX and PTX exhibited a better synergistic effect on MDR breast cancer cells than on non-MDR breast cancer cells. The in vivo study also showed that the multilayered nanosystem promoted MDR inhibition and synergy between chemotherapeutic agents, leading to significant tumor reduction in a xenograft animal model. Ch-MLNPs reduced the tumor volume by fivefold compared to that of the control group without causing overt cytotoxicity.