The 23 year old has two Scottish caps and joins fellow countrymen Neil Alexander and Steve Thompson at Ninian Park.
McNaughton has started 165 league games for Aberdeen and appeared in around 200 games all told.
"Following Glenn Loovens' signature, to secure another player of the stature so soon after the season has ended should be seen as a clear signal as to what our intentions are this summer," Sam Hammam told the official website.
"The fans can expect to see a pretty aggressive recruitment drive over this summer in order to back Dave Jones with the aim of reaching as high as possible and hopefully a top-six finish. I will do anything I can towards that eventuality.