The building in the capital, Amman, was sealed on the city governor's orders, an MB leader told Reuters news agency.
No reason was given for the closure, the official added.
The MB has a strong support base in urban areas and its political wing, the Islamic Action Front (IAF), is Jordan's largest opposition party.
The group split in 2014 into the old movement and a new, more moderate, officially licensed branch. The headquarters of the original movement were targeted in Wednesday's raid.
"We were surprised by this move from the Public Security Department," spokesman Badi al Rafaiah told Reuters.
"Many policemen and gendarmes came... broke the door down and threw out all the staff with an order to close down the main centre, which they sealed off without giving any explanation."
The rise in militant Islam in the region has increasingly strained relations between the Brotherhood and the authorities.
The IAF has boycotted parliamentary elections, alleging the system marginalises the party, while authorities have sporadically cracked down on the group.
Last year, a Muslim Brotherhood leader was jailed for criticising Jordan's ally the UAE, in the first such case involving a top opposition figure in Jordan for years.
Police in Jordan have shut the headquarters of the main opposition movement, the Islamist Muslim Brotherhood (MB), group officials say.