The significant threat posed by harmful microorganisms to human health and environmental sanitation has garnered considerable attention. Sepiolite, with its natural nanofibre structure, excellent physicochemical properties and good biocompatibility, shows great potential for antimicrobial applications in healthy living environments. In this study, magnesium oxide nanocrystal/sepiolite composites (MgO/sepiolite) were synthesized via an acid leaching–hydrothermal combined method using sepiolite without the addition of external magnesium salts, and their antimicrobial performance for bacteria and fungi was investigated. As both a magnesium source and carrier material, sepiolite effectively improved the dispersion of MgO nanoparticles by utilizing its large specific surface area, facilitating the formation of a greater quantity of smaller-sized MgO nanoparticles and abundant oxygen vacancies. The resulting MgO/sepiolite composites retained the fibre morphology of sepiolite, with the MgO nanoparticles uniformly dispersed on the fibre surface and with particle sizes in the range of 1.0–2.5 nm. The synergistic effects of these advantages of the MgO/sepiolite composite contributed to improved antimicrobial performance, leading to 99.99% antibacterial rates against Escherichia coli and Staphylococcus aureus, and a fungal growth grade of 0 against mixed fungi. Analyses of the pH value changes in the bacterial solution, Mg2+ release, free radical concertation and Fourier-transform infrared spectra data revealed that the excellent antimicrobial performance is primarily attributable to oxygen vacancy-mediated reactive oxygen species damage. Additionally, the release of Mg2+, pH adjustment and contact killing synergistically improved the oxygen vacancy-mediated damage, thus contributing to the antibacterial performance. This study is expected to provide valuable insights into the design and development of novel clay-based antimicrobial function materials, particularly with respect to synthesis methodology and the elucidation of antimicrobial mechanisms.