Barca have a 5-0 lead from last week's first leg at the Nou Camp and Luis Enrique has called up six players from the B team, including teenage Croatia midfielder Alen Halilovic, for the return game.
Playmaker Xavi and defender Thomas Vermaelen will miss the match due to injury, while centre back Gerard Pique and midfielder Ivan Rakitic are the only players included who started Sunday's 3-1 La Liga win at home to Atletico Madrid, Barca said on their website.
Barca are set to face Atletico in the quarter-finals as the La Liga champions take a 2-0 advantage over holders Real Madrid into their last 16, second leg at the Bernabeu stadium later on Thursday.
Barca's quest for silverware this season has been disrupted in recent weeks by off-field problems, with reports swirling about a rift between Luis Enrique and Messi.
Four-times World Player of the Year Messi is apparently unhappy with the coach's management style and tactics and said to be seeking an exit from the club he joined at the age of 13.
The Argentina captain responded by saying he was not thinking of leaving Barca but he has not explicitly denied claims his relationship with Luis Enrique has broken down.
Barca president Josep Bartomeu, who this month sacked sporting director Andoni Zubizarreta and called early elections for later this year amid criticism of his running of the club, played down the reports late on Wednesday.
"I have contact with him (Messi) and he is happy, with a lot of ambition and desire to win," Bartomeu told Catalan radio.
"He told me he wants to end his career at Barca and his commitment is absolute," Bartomeu added.
"There is no debate about his future, he already said he wants to stay and he has a contract here (until 2019)."
Asked about Messi's relationship with Luis Enrique, Bartomeu said: "We are closing this debate because it does not exist. I will not characterise his (the coach's) relationship with the dressing room, I am a discreet person."
Sevilla, Athletic Bilbao, Villarreal, Malaga, Espanyol and Getafe are already through to the last eight of the Cup and Barca would meet Villarreal or Getafe in the semi-finals if they advanced that far.
(Writing by Iain Rogers; Editing by John O'Brien)
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