The invention provides a medical composition for treating headaches and migraine, which is prepared from the following raw drugs by weight: 20-40 parts of concha haliotidis, 20-40 parts of nacre, 20-40 parts of ossa draconis, 20-40 parts of concha ostreae, 12-24 parts of radix paeoniae alba, 8-16 parts of angelica sinensis, 8-16 parts of largehead atractylodes rhizome, 8-16 parts of radix bupleuri, 12-24 parts of tuckahoe, 20-30 parts of uncaria rhynchophylla, 8-16 parts of negundo chastetree fruit, 7-13 parts of chastetree fruit, 7-13 parts of mint, 7-13 parts of ginger and 4-8 parts of liquorice. The invention also provides a preparation method and application of the medical composition. The medical composition provided by the invention can be used for effectively eliminating or greatlyrelieving traditional Chinese medicine syndromes such as hyperaction of liver Yang, liver fire flaming, deficiency of liver-yin and kidney-yin, blood stasis and the like and symptoms of headaches andmigraine caused by various diseases, and curing partial primary diseases of the headaches to a certain extent, therefore, a new approach is provided for the clinical medication.