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The application of α-mangostin (AMG) in breast cancer research has wide intentions. Chitosan-based nanoparticles (CSNPs) have attractive prospects for developing anticancer drugs, especially in their high flexibility for modification to enhance their anticancer action. This research aimed to study the impact of depolymerized chitosan (CS) on the cytotoxicity enhancement of AMG in MCF-7 breast cancer cells. CSNPs effectivity depends on size, shape, crystallinity degree, and charge surface. Modifying CS molecular weight (MW) is expected to influence CSNPs’ characteristics, impacting size, shape, crystallinity degree, and charge surface. CSNPs are developed using the method of ionic gelation with sodium tripolyphosphate (TPP) as a crosslinker and spray pyrolysis procedure. Nanoparticles’ (NPs) sizes vary from 205.3 ± 81 nm to 450.9 ± 235 nm, ZP charges range from +10.56 mV to +51.56 mV, and entrapment efficiency from 85.35% to 90.45%. The morphology of NPs are all the same spherical forms. In vitro release studies confirmed that AMG–Chitosan–High Molecular Weight (AMG–CS–HMW) and AMG–Chitosan–Low Molecular Weight (AMG–CS–LMW) had a sustained-release system profile. MW has a great influence on surface, drug release, and cytotoxicity enhancement of AMG in CSNPs to MCF-7 cancer cells. The preparations AMG–CS–HMW and AMG–CS–LMW NPs considerably enhanced the cytotoxicity of MCF-7 cells with IC50 values of 5.90 ± 0.08 µg/mL and 4.90 ± 0.16 µg/mL, respectively, as compared with the non-nano particle formulation with an IC50 of 8.47 ± 0.29 µg/mL. These findings suggest that CSNPs can enhance the physicochemical characteristics and cytotoxicity of AMG in breast cancer treatment.