The invention relates to an organically modified and metal ion-loaded anti-microbial alpha-ZrP powder and a preparation method thereof. Alpha-ZrP is used as a base material, micromolecule amine is used for pre-intercalation, so that active forces between alpha-ZrP laminates are reduced and interlayer distances are increased; furthermore, a silane coupling agent is inserted into laminates; heat treatment is carried out for removing micromolecule amine which is used for pre-intercalation; a reaction is carried out between terminal sulfhydryl of the silane coupling agent and metal ions, and the organically modified and metal ion-loaded anti-microbial alpha-ZrP powder is prepared. Initial decomposition temperature of the organically modified and metal ion-loaded anti-microbial alpha-ZrP powder is 340-450 DEG C, the interlayer distance is 1.60-1.90 nm, grafting rate of the coupling agent is 6-18%, and metal content is 1-15%. The organically modified and metal ion-loaded anti-microbial alpha-ZrP powder has the advantages of higher heat stability, grafting rate, interlayer distances and metal content, extremely high affinity with nonpolar organic substances, and uniform dispersion in hydrophobic organic polymer materials; the powder can be added into most high-molecular materials (PET, PBT, PP, etc.) which are processed by fusion for preparing flame-retardant and anti-microbial functional materials.