The toponym appears to refer to the "Middle Town" of a group.
The Domesday Book of 1086 records that Remigius de Fécamp, Bishop of Lincoln held a large estate of 31 hides of land at Great Milton. The estate had presumably belonged to the Diocese of Dorchester, of which Remigius had been consecrated bishop in 1070. The see of Dorchester had been absorbed into that of Lincoln in 1072, and Remigius had been translated to Lincoln as bishop of the newly united diocese.
The Domesday Book lists two water mills in the parish. By the time of the Hundred Rolls in 1279 there was a third watermill and in about 1500 there was a fourth mill. There is no known subsequent record of the third and fourth mills, but both of the others seem to have survived until the 17th and in at least on case the 18th century. By the 19th century both mills were disused. In 1322 there was at least one windmill in the parish, and possibly two. The parish still had two windmills in 1838 and about 1900.
In 1762 a fire destroyed 16 houses in the village.