The invention provides a compound propolis composition used for treating pig viral diarrhea and a preparation method thereof and relates to the field of animal medicine. The preparation method provided by the invention comprises the following steps of: (1) respectively carrying out superfine grinding on various components (except for interferon) in a prescription, and respectively sieving by virtue of a 700-mesh sieve; (2) weighing 15-35 parts by weight of propolis, 10-20 parts by weight of porcine interferon, 10-35 parts by weight of granatum, 15-40 parts by weight of fructus chebulae, 10-40 parts by weight of scutellaria baicalensis, and uniformly mixing for 5-10 minutes; (3) weighing 10-35 parts by weight of dark plum, 10-35 parts by weight of Chinese knotweed herb, 15-35 parts by weight of round cardamom, 15-35 parts by weight of dried ginger, 15-35 parts by weight of potentilla chinensis, and uniformly mixing for 5-10 minutes; and (4) mixing compositions obtained by the steps (2) and (3), and continuously mixing uniformly for 10-15 minutes, thus the compound propolis composition is obtained. The compound propolis composition provided by the invention has the beneficial effects that the prescription is reasonable, the preparation method is simple, the compound propolis composition has no toxic or side effect, no pollution, no drug residue and no drug resistance, the superfine grinding efficiency and the biological availability are high, the curative effect is obvious, and clinical application shows that the compound propolis composition achieves a special effect when being used for treating pig viral diarrhea.