Morton parted company with Jim Duffy at the end of the season, which saw them finish a disappointing seventh in the Scottish Championship.
McKinnon has been out of work since leaving Tannadice in October.
The 47-year-old has also managed Raith Rovers and Brechin City.
He helped Raith and Dundee United reach the second-tier play-offs during his time in charge, but was unable able to secure a place in the Premiership for either.
One of United's victims in the 2016-17 play-offs was a Duffy-managed Morton, but they could not get past Hamilton in the play-off final.
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