The 25-year-old opening batsman will step in for usual captain Kane Williamson, who has commitments in the Indian Premier League (IPL).
Vice-captain Tim Southee will also still be playing in the IPL when the triangular series starts in Ireland on May 12.
"Tom has been a leader within the side for a while now and this is a chance to continue his development in that area," selector Gavin Larsen said in a statement.
"It's a great learning opportunity for Tom and a chance for other squad members to take on a bigger leadership role too."
Fast bowler Seth Rance and all-rounder Scott Kuggeleijn, who was drafted into the test squad last month but did not play, could make their ODI debuts during the series.
Pace bowler Neil Wagner, who was named New Zealand's Test Player of the Year last week, could also make his ODI debut during the series.
"This is a fantastic opportunity to give new players a taste of international cricket, as well as reward guys who have pushed their way back into contention," said Larsen.
Pace bowler Hamish Bennett and batsman George Worker have also returned to the squad.
The Champions Trophy starts in England on June 1.
Squad: Tom Latham (captain), Hamish Bennett, Neil Broom, Scott Kuggeleijn, Colin Munro, James Neesham, Henry Nicholls, Jeetan Patel, Seth Rance, Luke Ronchi, Mitchell Santner, Ish Sodhi, Ross Taylor, Neil Wagner, George Worker
