The invention discloses a Houttuynia cordata injection and a preparation method thereof, and the Houttuynia cordata injection is prepared by the following method: taking fresh Houttuynia cordata, carrying out water vapor distillation, collecting initial distillate, carrying out re-distillation, collecting re-distillate, adding 4-25g of hydroxypropyl-beta-cyclodextrin and 7-9g of sodium chloride into each 1000ml of re-distillate, and preparing the injection according to the conventional method. The preparation method takes the Houttuynia cordata injection as a research object, seeks harmful components/allergic sources which can cause adverse reactions, investigates the allergic mechanism, improves the production process and successfully develops the new safe Houttuynia cordata injection.