The invention discloses a peganum harmala lipid transfer protein (PHP) and relates to the preparation and use of new protein with antifungal, anticancer and antivirus activities. The method uses seeds of a peganum harmala plant as raw materials and comprises the following steps: preparing a coarse product, performing cationic exchange chromatographic separation and purifying by using a molecular sieve; and gradually separating and collecting a purified component having antibacterial activity, dialyzing, desalting, freeze-drying and thus, obtaining purified PHP. In the invention, a filter paper disc agar diffusion method is adopted, and researches prove the protein has growth inhibiting effect on five plant pathogenic fungi, namely alternaria alternate, penicillium degitatum, rhizopus stuolonifer, magnaporthe grisea and penicillium italicum. An 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method proves that the protein has inhibiting effect on proliferation of human esophageal carcinoma cell Eca109, human cervical cancer cells HeLa, human stomach cancer cells MGC-7, mouse melanoma cells B16 and the like. The protein can inhibit the activity of human immunodeficiency virus 1 (HIV-1) reverse transcriptase. The protein can be used for developing medicines for resisting agricultural pathogenic fungi, tumors and viruses.