Fresh from scoring against Barcelona at the weekend, Chukwueze got Villarreal’s fifth goal of the game in the 50th minute.
He has now scored three goals in all competitions for Unai Emery’s tutored in the current campaign.
Alberto Moreno scored a brace within the first 30 minutes to put Villarreal in control of the game.
Mandy and Paco Alcacer scored the third and fourth goals in the 28th and 37th minutes respectively.
Chukwueze, Gerrard Moreno, Boulaye Dia, and Nikita Iosifov all scored in the second half to give Villarreal an emphatic victory.
Villarreal who hasn’t won Copa del Rey title in their 98-year history has now matched on to the next round.