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A nanocomposite microneedle (ZCQ/MN) patch containing copper/zinc dual-doped mesoporous silica nanoparticles loaded with quercetin (ZCQ) was developed as a combination therapy for androgenic alopecia (AGA). The degradable microneedle gradually dissolves after penetration into the skin and releases the ZCQ nanoparticles. ZCQ nanoparticles release quercetin (Qu), copper (Cu2+) and zinc ions (Zn2+) subcutaneously to synergistically promote hair follicle regeneration. The mechanism of promoting hair follicle regeneration mainly includes the regulation of the main pathophysiological phenomena of AGA such as inhibition of dihydrotestosterone, inhibition of inflammation, promotion of angiogenesis and activation of hair follicle stem cells by the combination of Cu2+ and Zn2+ ions and Qu. This study demonstrates that the systematic intervention targeting different pathophysiological links of AGA by the combination of organic drug and bioactive metal ions is an effective treatment strategy for hair loss, which provides a theoretical basis for development of biomaterial based anti-hair loss therapy.