The invention relates to the technical field of biological medicines, in particular to a micromolecular water cluster composition and a preparation method thereof. According to the invention, the micromolecular water cluster composition is prepared from micromolecular water and biological enzyme, and the selected specific biological enzyme can stabilize the micromolecular water for a long time. Meanwhile, the micromolecular water cluster composition prepared by the preparation method disclosed by the invention can be used for promoting keratinocyte end differentiation and up-regulation expression of transcriptional levels of intercellular connexin and keratinocyte envelope protein so as to achieve an effect of enhancing skin barrier, can remarkably improve anti-microbial humoral response,humoral immune response, antibacterial peptide-mediated anti-microbial humoral immune response, bacterial response, bacterial defense response and defense response related genes for other organisms, and has an immune regulation effect.