The invention discloses a pharmaceutical composition for controlling citrus gonggan canker. The pharmaceutical composition comprises the following raw materials: purslane, tea tree leaf, pyrethrum, lettuce, weeping willow leaf, piper methysticum forst, tea tree leaf, anabasis aphylla, potassium salt, phosphorus salt, nitrogen salt, calcium salt, iodine salt, boron salt, molybdenum salt, zinc salt, manganese salt, copper salt, iron salt, vitamin, amino acid, indolebutyric acid, gibberellins, 6-benzyladenine, naphthylacetic acid, agar, kinetin, N-methyl pyrrolidone, dinonyl sodium naphthalene sulfonate, DUPONT EEA2112AC compatilizer, earthworm powder, alkyl sulfate potassium, trimethylolpropane triacrylate, 3-aminopropyltriethoxysilane, carrageenin, mancozeb, streptomycin, prochloraz, wetting penetrating agent, synergist, and ethanol. The pharmaceutical composition disclosed by the invention is used for controlling the citrus gongan canker, and can improve the yield and the sugar content; and citrus gonggan is good in mouthfeel and high in quality, which are higher than the use effect of a conventional pharmaceutical composition for controlling the citrus gonggan canker.