The Wales international has impressed during loan spells at Northampton Town and Birmingham City over the past two seasons and has now secured his future at the Etihad Stadium until 2016.
Huws joined City in 2009 and Patrick Vieira, head of the club's elite development squad, backed the 20-year-old's temporary switch to Wigan.
"I'm really pleased that Emyr is going to continue his development as a player under a manager who knows City so well," Vieira told City's official website. "Uwe [Rosler] knows perfectly how the club works and how we like to play.
"Emyr is a great talent of this club which he proved on loan at Birmingham City last year – he showed that he can play at Championship level but this time it will be a different challenge.
"Whereas last year, he was fighting against relegation with Birmingham, this time he's going to a club expecting to win and aiming to win promotion, so I'm really pleased he's both agreed to stay on at City until 2016 and that he's taken this opportunity Wigan have offered him."
Rosler added: "City are looking for Emyr to develop and as we have demonstrated in the past, top young players are able to come to us and improve, both on the field with regular playing time, but also off the field in terms of absorbing our first-team training culture and discipline and helping them to improve every facet of their professional life."
