The 32-year-old from Bristol won his first title defence emphatically at Cardiff's Ice Arena after being crowned champion out of the ring last year.
He beat 24-year-old Morales - younger brother of the multi-weight world champion Erik - 118-110 on two of the judges' cards and 119-108 on the other.
Haskins said: "It's absolutely amazing. I am flying at the moment."
Haskins was due to box Randy Caballero for the title last November but was crowned champion when the American was stripped of the belt after failing to make the weight.
He now wants an all-British title fight with former IBF champion Stuart Hall, who lost to Haskins in 2012.
"All I was thinking during the training for this fight was about Stuart Hall," said Haskins.
On the undercard in Cardiff, Welshman Andrew Selby won the British flyweight title with a unanimous points victory over Leicester's Louis Norman.
Lee Haskins retained his IBF world bantamweight title with a unanimous points win over Mexico's Ivan Morales.