The 30-year-old will lead the Indomitable Lions at the June 21-July 19 championship in Egyp, where they have been pitted against Ghana, Benin and Guinea-Bissau in Group F.
The announcement was made at a press conference by the Cameroon Football Federation on Wednesday.
The Lions have been without a permanent captain since the appointment of Dutchman Clarence Seedorf as head coach in August last year.
Benjamin Moukandjo, who led the side to clinch gold at the 2017 Afcon in Gabon, held the armband until Seedorf's appointment when the striker announced retirement from international duty in September, due to the coach's decision to sideline players plying their trade in lower leagues like the Chinese Super League.
Choupo-Moting heads to Afcon on the back of his maiden season with Ligue 1 champions PSG, where he made 22 league appearances, starting eight of the matches and scoring thrice.
It will be the 30-year-old German-born's second appearance at Afcon following his debut in 2015. He excused himself from the 2017 championship, which the Lions eventually won.
Cameroon open their campaign against Guinea-Bissau on June 25 before facing four-time champions Ghana, and Benin June 29 and July 2, respectively.
The Lions are hoping to claim a sixth title.