Provided is a method of extracting and separating zirconium and hafnium from hydrochloric acid medium, which relates to the technical field of fine separation of substance. Primarily, extraction is performed to acidic raw liquid containing zirconium compounds by a synergistic extraction system consisting of DIBK and phosphonic acids extraction agent, so that the zirconium goes to the aqueous phase and the hafnium goes to the organic phase, thus the separation is achieved. No toxic substance is involved throughout the process, so clean production is achieved.