Aberrant interactions of metal ions with amyloid-β peptide (Aβ) can potentiate Alzheimer's disease (AD) by participating in the aggregation process of Aβ and in the generation of reactive oxygen species (ROS). Metallothionein-3 (MT3), which is aberrantly expressed in AD brains, is believed to play an important role in the AD progression due to its ability of maintaining metal homeostasis and scavenging ROS. However, the related molecular mechanism is not clear. In this work, the metal-dependent interactions of MT3 β-domain (βMT3) with amyloid-β peptide (Aβ) were systematically studied. The results showed that Zn3−βMT3 has a higher affinity to Aβ (Kd: ~0.7 μM) than Cu4−βMT3 (Kd: ~22 μM). In Zn3−βMT3, both Pro7 and Pro9 face outwards with their five-member rings in parallel, favoring their binding with aromatic residues via CH/π interactions. Two aromatic residues (Phe4 and Tyr10) in Aβ were identified as the specific binding sites for βMT3. Based on these, we posit a characteristic in-situ protection role of Zn-MT3 in inhibiting the Cu2+-induced Aβ neurotoxicity, in which stable Zn−MT3/Aβ complex forms via the Zn3−βMT3/Aβ interaction and effectively prevents the formation of Cu−Aβ in high viscosity physiological fluids. Our results provide the mechanistic pathway and the specific roles of βMT3 in its protective bioactivity against AD progression, which means significant for elucidating the function of MT3 in AD neuropathology and for designing a MT3-related therapeutic strategy for AD.