Under the JCPOA, the Islamic Republic agreed to severe limitations on their uranium supply, as well as not using more advanced centrifuges for uranium enrichment.
With the tensions between Donald Trump and Rouhani, Khamenei still remains the leader of Iran.
Larijani did not elaborate on what those changes would be.
"If one day they want to prevent the export of Iran's oil, then no oil will be exported from the Persian Gulf," Rouhani said.
"We are the strongest economy in the world ... and if we cut you off then you collapse."
The Iranian President said that US withdrawal from the accord was a "violation of morals."
There are four major flaws in the agreement that must be addressed if it is to have any chance of keeping the world’s most dangerous weapons out of the hands of the world’s most dangerous regime.
"Our response will be stronger than what they imagine and they would see that within a week," threatened Rouhani. Iran's nuclear chief said 20% uranium enrichment can resume in days.
The Islamic nation currently holds the region's largest arsenal of ballistic missiles.
Iran's Foreign Ministry said the move "crossed all red lines of conduct in the international community... and will surely be answered by a serious reaction of the Islamic Republic."