The name Morton is from the Old English Mor+tun, or "Farmstead on the moor or marsh". In the 1086 Doomsday Book, the village is given as Mortun. Over the years the village has also been known as Morton-by-Bourne and Morton-Cum-Hanthorpe.

Hanthorpe was known as Hermodesthorp at the time of the Doomsday survey. This was a Scandinavian  name meaning the "Outlying farmstead or hamlet of a man called Heremod or Hermothr"

The parish registers for Morton and Hanthorpe date back to 1549.

St John the Baptist Church was largely built in the 14th & 15th centuries but parts of the church date back to an earlier building built in the 12th century. The total area of Morton and Hanthorpe in 1911 was listed as 4849 acres and had a population of 839 people. .

Census of (2001) the population was  2,352 people. Breakdown in age as below

Morton school was founded in the early 1800's and in 1863 took over a permanent site in the High Street which was formerly the workhouse.  By 1870 the school had been extended and was now capable of holding 135 mixed pupils. 

Morton school was founded in the early 1800's and in 1863 took over a permanent site in the High Street which was formerly the workhouse.  By 1870 the school had been extended and was now capable of holding 135 mixed pupils. 

The Roman built Car Dyke runs on the edge of the fens and passes Morton to the east. The Car Dyke originally linked the River Nene at Peterborough with the River Witham near Lincoln.

Salt making has been carried out in the fenland area where its low rainfall and drying winds, were the ideal conditions for the collection of sea salt by evaporation. Salt making was carried out from late Iron Age to Roman times with Morton being one of the larger excavations found in East Anglia.

Morton was a stop on the Bourne branch line of the Great Northern Railway and opened to goods traffic in 1871 with the first passenger service opened on 2nd June 1872. The last scheduled passenger service ran on the line on 22nd September 1930 with special services running until the 1950's and goods traffic until the 1960's.

The oldest of the three public houses is The King's Head which dates back to 1703.

Hanthorpe once had a Windmill that supplied flour to the villages, but production ceased by 1911 although the mill remained on the site.

The common land was enclosed by the enclosure act of 1768 with the enclosure award of Morton and Hanthorpe completed in 1771. This act also included the drainage of common lands before they became enclosed.