The invention provides a medical instrument rapid sterilizing agent which comprises the following components in percentage by weight: 0.1-2% of sodium dichloroisocyanurate, 5-15% of sodium silicate, 2-10% of sodium phosphate, 0.5-5% of boron nitride, 1-5% of complexing agent, 0.5-2% of corrosion inhibitor, 0.2-1% of enhancer, 0.1-2.5% of stabilizer, 0.1-2.55% of penetrant and the balance of water.The invention also provides a preparation method of the medical instrument rapid sterilizing agent, which comprises the following steps: heating and mixing the sodium dichloroisocyanurate, sodium silicate, sodium phosphate and boron nitride at 60-70 DEG C for 1-3 hours, cooling, adding the stabilizer, the penetrant, EDTA-2Na, pentaerythritol ester and sodium metasilicate, adding water to 100%, and uniformly mixing to obtain the sterilizing agent. The medical instrument can be sterilized with a stock solution within 30 minutes, and can be disinfected within 5 minutes. The medical instrument rapid sterilizing agent disclosed by the invention can be used for killing enteropathogenic bacteria, pyogenic coccus, pathogenic saccharomycetes, bacterial spores, aspergillus niger and mycobacterium tortoise, can be used for inactivating viruses, and has the advantages of high efficiency, quick effect, safety, simplicity, convenience and no corrosion.