A drug combination prediction method comprising: storing a plurality of original gene sets, at least one first gene impacted by a first drug and at least one second gene impacted by a second drug; determining the part of the at least one first gene and the part of the at least one second gene to be a first interaction gene set; calculating a gene amount of the first interaction gene set to obtain a first interaction gene amount, and calculating a first percentage generated by the first interaction gene amount in the first original gene set; calculating an interaction value of the combination of the first drug and the second drug according to the first percentage; and selecting at least one synergistic pharmaceutical composition according to the interaction value.