The invention relates to a method for preparing calcium sulfate crystal whiskers (CaSO4) by using impurity-containing gypsum as a raw material. The method comprises the following steps of: removing main impurities in the raw material which is the low-priced impurity-containing gypsum resource in a mode of roasting, acid-complex leaching and alkaline leaching and simultaneously thinning crystal grains to obtain a superfine dihydrate calcium sulfate precursor which is high in purity and dispersibility; and preparing the anhydrous calcium sulfate crystal whiskers with a length of 20 to 2,000mu m, a diameter of 0.5 to 20 mu m, a length-diameter ratio of 40 to 1,000 and a weight percent content of over 95 percent in a mode of hydrothermal conversion-roasting of a fluxing agent. The method has the advantages of low-priced and easily bought raw materials, simple process, wide application range, and high added value. The calcium sulfate crystal whiskers prepared by the method have a big length-diameter ratio and regular shape, and can be used as reinforcing, heat insulating or flame retardant materials in industries of plastics, rubbers, coatings, papermaking, building materials and the like.