The present invention discloses a modified calcium sulfate crystal whisker papermaking filler, a preparation method and applications thereof, wherein a modified calcium sulfate crystal whisker papermaking filler is prepared, and then the modified calcium sulfate crystal whisker papermaking filler is applied in papermaking industry. The application of the modified calcium sulfate crystal whisker papermaking filler in the papermaking industry comprises: 1) selection a papermaking slurry, (2) use of the modified calcium sulfate crystal whisker papermaking filler and related auxiliary materials, 3) papermaking, and 4) white water circulation. According to the present invention, the calcium sulfate crystal whisker raw material source is wide, conditions are wide, and solid waste pollution can be effectively solved; the modified calcium sulfate crystal whisker product has characteristics of high whiteness, low abrasion, effectively-controlled solubility, high papermaking retain rate, and low white water load, the problem of pipe scale is eliminated, and the product can completely replace calcium carbonate, kaolin, talc powder, and other papermaking fillers, and partial plant fiber raw materials; and the method has characteristics of low equipment investment, simple modification process, strong operability and low cost, and is applicable for large scale production.