Hawaii says the policy discriminates against Muslims and hurts the state's tourist-dependent economy. The implied message in the revised ban is like a "neon sign flashing 'Muslim ban, Muslim ban'" that the government didn't bother to turn off, state Attorney General Douglas Chin told the judge.
Trump's first ban and the revised one have both been criticized as amounting to a ban on entry of Muslims into the U.S.
Hawaii's attorney general Chin praised the court ruling.
"With a preliminary injunction in place, people in Hawaii with family in the six affected Muslim-majority countries - as well as Hawaii students, travelers, and refugees across the world - face less uncertainty," he said.
"While we understand that the President may appeal, we believe the court's well reasoned decision will be affirmed," he added in a statement.
In his first order, Watson ruled it was plausible "to conclude that targeting these countries likewise targets Islam" given their Muslim populations ranging from 90.7 percent to 99.8 percent.
Trump has said a travel ban is needed to preserve U.S. national security and keep out extremists.
If the Justice Department appeals the latest ruling it will be heard in the same San Francisco-based court that upheld a halt to Trump's first travel ban in February a after a judge in Seattle ruled against it.