According to "A Brief Guide to Great Milton", published by the Great Milton & District Local History Society, the name of the village means the "middle town" of a group-Domesday Book refers to it as Middeltone.  It was an obvious place for settlement due to the abundance of water, not only the river, but also underground streams on the rising ground to the north of the initial settlement around the church.  Domesday Book mentions 2 water-mills, and later there were another 2.  The village's Enclosure Award was a late one, being made in 1845, so more than usual is known about the Common Land.  For example, what is now known as Milton Common had been "Harrington Field" running across the north of the parish.

The church is dedicated to St. Mary, and was originally a small nave and chancel built shortly after the Norman Conquest.

The church was damaged by  fire sometime during the 13th century.

But during the 14th century, the north and south aisles were added and the chancel enlarged-at this time the church served a parish including the villages of Chilworth Valery, Chilworth Muzzard, the hamlet of Combe, and to the south Little Milton and the Manor of Ascott.

The Tower was also built at this time.

The church underwent restoration work in 1850 costing £2000.