Huws initially moved to the DW Stadium last month on loan just after signing a new long-term deal with the reigning Premier League champions.
The 20-year-old has featured in every game so far this season for the Latics and boss Uwe Rosler is delighted to have secured his services, after earlier signing Denmark international William Kvist, Brentford midfielder Adam Forshaw and striker Andy Delort from French side Tours.
They did, however, lose key midfielder James McArthur to Crystal Palace for an undisclosed, significant, transfer fee.
“Emyr has impressed everyone since arriving at the club and we feel that he can have a major role to play in the future of the club," Rosler said.
“Everybody can see what a very talented player Emyr is, and from the first training session with us leading through to the games he has played, he has been very good.
“At just 20 years old he is already with the full Welsh national team and the chance to sign him on a long-term contract was too good an opportunity to turn down.
“It is so encouraging that we have been able to sign three players today in their early 20s, it signals exactly what the long term intentions of the club are because these players will become the face of our team in the future.”
Huws added: “I have really enjoyed my time at Wigan Athletic and working with Uwe Rosler, where I think the future is bright and a place I can really develop.
“I need to thank him for believing in me and I also need to thank everyone at Manchester City who have played a part in my development over the years. I now look forward to the challenge ahead as we pursue a return to the Barclays Premier League.”