Through his father's influence, in 1639 he married Lady Henrietta Gordon, daughter of the Marquess of Huntly, with whom he made a great match and by whom he had four sons, of whom George succeeded his grandfather as fourth Earl of Winton, and the others died young or without issue.
Seton showed great military abilities and was firmly attached to the Royalist cause.
Seton suffered great hardships at the hands of the rebels during the English Civil War, and his father had to sell long-held family estates in Linlithgowshire, that of Niddry Castle and one at Winchburgh, to rescue him from imprisonment.
He died at Seton Palace on 4 June 1648, prematurely and unexpectedly of an illness probably caused by his imprisonment, predeceasing his father.
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