The invention discloses a binding protein combination for detecting plasmodium falciparum HRP2 and plasmodium vivax LDH and a preparation method and application thereof. The binding protein combination is composed of a binding protein 1 and a binding protein 2 which detect the plasmodium falciparum HRP2 and a binding protein 3 and a binding protein 4 which detect the plasmodium vivax LDH, and amino acid sequences of the binding protein 1, binding protein 2, binding protein 3 and binding protein 4 are shown in SEQ ID NO:5-8. According to the binding protein combination and the preparation method and application thereof, a phage display technology is adopted, the plasmodium falciparum HRP2 and the plasmodium vivax LDH are taken as target antigens, and the binding protein combination with high affinity and good specificity is selected from a phage display protein library. A genetic engineering technology is used for recombinant expression and purification, a binding protein combination reagent replaces an antibody reagent for malaria immunodetection, a colloidal gold chromatography rapid detection method is established, the storage stability of an obtained kit is higher than that of an existing clinical detection product, and the binding protein combination has the advantages of being reliable, accurate, safe, simple, convenient and stable.