Doughty, 23, spent part of the 2015-16 season with the Robins and scored five goals in 20 starts as they finished 16th in League One.
He joins from Championship side Queens Park Rangers, having also been on loan at fellow League One side Gillingham.
Jones, 20, joins from Liverpool, and made two appearances while on loan at Blackpool in League One last season.
Meanwhile, former Swindon midfielder Alan McLoughlin has been appointed as the club's new under-18s manager.
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Swindon Town have signed midfielder Michael Doughty and defender Lloyd Jones on season-long loan deals.