The aim of this research is to investigate the influence of different functional groups of β-cyclodextrin (CD) in functionalizing gold nanoparticles. The functionalized nanoparticles are then utilized for loading the 5-fluorouracil (5-FU) drug and evaluating their in vitro anticancer activity. For this purpose, a two-step method was employed to synthesize Mono-6-(1,3-trimethylenediamine)-6-deoxy-β-cyclodextrin (TMACD), which was further utilized for fabricating gold nanoparticles (AuNPs) using ultrasound-assisted synthesis. The loading of 5-FU was compared among three cyclodextrin derivative, namely β-cyclodextrin ([email protected]/CD), [email protected]/CD, 2-hydroxylpropyl-β-cyclodextrin ([email protected]/HPCD), and TMACD ([email protected]/TMACD). Among them, the nanocomposite AuNPs/TMACD exhibited the highest associate efficiency and loading efficiency which were confirmed by analytic techniques such as FTIR, PXRD, TEM. Moreover, the release behavior of 5-FU from the nanocomposites was investigated at pH 7.4, revealing that all AuNPs/CDs nanocomposites effectively protected the drug with a low release percentage ranging from 23.13% to 29.45%. Docking model analysis indicated that the 5-FU ligand formed six hydrogen bonds and interacted favorably with the HPCD molecule. In the in vitro cell viability assay, both nanocomposites, [email protected]/CD and [email protected]/TMACD, not only demonstrated effective anticancer activity against breast cancer cells (MCF-7) but also exhibited minimal toxicity towards normal cell lines. Remarkably, the results revealed that [email protected]/TMACD displayed the highest efficacy in suppressing the growth of the breast cancer cells. These findings highlight the considerable potential of amine-derivative cyclodextrin-capped AuNPs as exceptionally efficient carriers for anticancer drugs, offering promising applications in both diagnosis and therapy.