Jordan, which borders Iraq's Anbar province, much of which has been overrun by IS, is one of several countries taking part in US-led air strikes against the jihadist group that began in Iraq but has since been expanded to Syria.
Abadi met separately with King Abdullah II and Prime Minister Abdullah Nsur.
He briefed Nsur on what he called "security and terrorist challenges facing Iraq, particularly ones from Daesh which is destroying Iraqi civilisation," Jordan's state news agency Petra said.
Abadi told Nsur that "increased cooperation" was needed between Baghdad and Amman to crush the jihadists who pose a "threat to the entire region".
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"Our vision for the future is to develop political, economic and trade ties" also, he said, according to Petra.
Nsur told his guest that Jordan wants to see an Iraq which is "strong, not torn apart, so that it can be a support" for all Arab countries.
King Abdullah also pledged Jordan's "full support" for Baghdad and the US-led coalition "in confronting terrorist organisations", the palace said.
His visit to Jordan comes shortly after a trip to Iran, Iraq's neighbour to the east, during which Abadi also discussed the fight against IS.