Former Cardiff City boss Mackay - who was appointed by Wigan in November - and their ex-head of recruitment Iain Moody were reported to the Football Association (FA) in August over the exchange of alleged racist, sexist and homophobic text messages.
The pair were said to have made derogatory comments about South Korea international Kim in a text when he first signed for Cardiff in July 2012.
Kim's agent Lee Yeung-joong later insisted that the midfielder received no unfair treatment at the hands of Cardiff or Mackay, who Lee has again praised following the announcement of his client's move to the Championship club.
"When Kim Bo first joined Cardiff in 2012, Malky showed him so much warmth and understanding and helped him integrate into the British culture, on and off the field," Lee told Wigan's official website.
"This experience made the decision to come to Wigan now a very easy one."
Kim - released by Cardiff last month - added: "I am very happy to be joining up with the gaffer again. I really enjoyed working with him in the past and he helped me so much in my career.
"He gave me the chance to fulfil my dream of playing in England and I am now looking forward so much to working with him again.
"Since becoming a free agent, we had various offers but when the chance came to be with the gaffer again at Wigan, this really was the only place I wanted to come."
The FA investigation into Mackay and Moody is still ongoing, while Wigan chairman Dave Whelan was banned from football for six weeks and fined £50,000 in December for insulting comments he made about Jewish and Chinese people.
Kim joins Wigan with the club second-bottom of the Championship, seven points adrift of safety.
