The US state department’s move follows Moscow’s reduction of US diplomatic staff in Russia last month.
That in turn followed new US sanctions on Russia over Crimea and alleged election interference, which led to the expulsion of 35 Russian diplomats.
President Barack Obama had ordered those expulsions, along with the closure of two compounds, last December.
Although Russian President Vladimir Putin did not respond initially to that move, with Mr Trump set to assume office, he then announced on 31 July a reduction of 755 US diplomatic staff in Russia, in retaliation for the US sanctions.
The US diplomats expelled have until this Friday to leave Russia – a day before the US closures of the Russian consulate and two annexes, which are trade missions, must be completed.
A senior administration official said on Thursday that the consulate and the residence attached to it as well as the two trade missions would close but no Russian staff would be required to leave the country.
Russia will be allowed to maintain the properties, but not use them, the official added.
The state department said the US actions were “in the spirit of parity”. It blamed Moscow for what it called a downward spiral in bilateral ties, but suggested it wanted an end to the current spat.
“The United States hopes that, having moved toward the Russian Federation’s desire for parity, we can avoid further retaliatory actions by both sides and move forward to achieve the stated goal of both our presidents: improved relations between our two countries and increased co-operation on areas of mutual concern,” state department spokeswoman Heather Nauert said in a statement.
The move leaves each country with three consulates in place, Ms Nauert added.
Russian Foreign Minister Sergei Lavrov spoke to US Secretary of State Rex Tillerson in a phone call on Thursday, expressing “regret at the escalation of tensions in bilateral relations”.
He said Moscow would study the order and respond accordingly, according to a statement from the Russian foreign ministry.
Mr Lavrov and Mr Tillerson are due to meet in September on the sidelines of the UN General Assembly in New York.
Earlier this month, Mr Trump said US relations with Russia were at a “dangerous low” amid a row with Congress over the fresh sanctions against Moscow.
The president, who wanted warmer ties with Russia, had opposed the bill, which included a provision that limits his ability to lift sanctions and forces him to consult Congress first.
Mr Trump has been dogged by claims that Russia tried to sway the election in his favour and several investigations are under way to determine whether anyone from his campaign colluded with Moscow.
But the Kremlin has repeatedly denied interfering and Mr Trump has insisted that there was no collusion, calling the investigations a “witch hunt”.