The invention discloses a compound preparation for preventing and controlling tree rot disease as well as a preparation method and application of the compound preparation. The compound preparation is prepared from the following raw medicinal materials: caulis hippophae rhamnoides, radix ampelopsis, herba chrysosplenii carnosi, cortex pyri betulaefoliae, cayratia trifolia, herba polygoni capitati, herba elatostematis laevigati, herba veronigastri caulopteri, folium callicarpae pedunculatae, herba procris wightiana, adeps marmotae, borax, margarita radix, white granulated sugar, minium, olibanum, radix angelicae dahuricae, beeswax, galla chinensis, rhizoma paridis, fructus cnidii, radix arnebiae, herba lobeliae chinensis, radix sophorae flavescentis, myrrha, squama manitis, radix trachycarpi, rhizoma atractylodis, flos sophorae immaturus, fructus mume, synergistic phosphorus and water. The compound preparation has effects of sterilizing, inhibiting bacteria, accelerating cell division, promoting tissue healing and stimulating plant growth, special effects on prevention and control of tree rot disease, dry rot, root rot, gummosis and various tree pruning wounds, a preventing and controlling rate of 99%, a curing rate of 90%, stable preventing and controlling effects, no resistance and toxic side effects, and effects much better than biocides.