The invention discloses a fruit stem rooting agent. The fruit stem rooting agent is prepared from yellow soil, indole-3-butyric acid potassium, sodium alpha-naphthyl acetate, GGR, sphagnum moss leaching liquor, red floating powder, alligator weed powder, white sugar, pine needle powder, revolution, lushan mountain barberry root powder, indoleacetic acid, magnesium chloride hexahydrate, sodium bicarbonate, calcium hydroxide, activated carbon, citric acid, myristic acid, sodium thiosulfate, glyceryl tristearate, sucrose ester, sodium tartrate, sodium sorbate, lignin, thiabendazole, fiveleaf gynostemma herb, rhizoma bletillae glue, tea polyphenol and ethylhexyl ferulate. The invention also provides a preparation method of the fruit stem rooting agent. The prepared fruit stem rooting agent is strong in rooting capability, can promote fruit stem rooting and improve the fruit stem rooting efficiency and quality, and can inhibit bacteria breeding and prevent fruit stem root rotting in the rooting process.