The FSB said it was investigating all 22 members of the Russian Antiwar Committee - a group of politicians, business people, journalists, lawyers, artists and academics all based outside the country, who oppose Russia's war in Ukraine.
Apart from Khodorkovsky, the group includes prominent dissident Vladimir Kara-Murza, former world chess champion Garry Kasparov and ex-prime minister Mikhail Kasyanov.
The FSB statement referred to the group as "Khodorkovsky and his accomplices," implying it viewed him as the main figure.
The move came less than two weeks after the Parliamentary Assembly of the Council of Europe, a human rights forum of MPs from 46 European countries, said it was creating a "platform for dialogue" with Russian democratic forces in exile, in which Khodorkovsky said he aimed to participate.
Russia quit the Council of Europe in 2022 while facing expulsion over the invasion of Ukraine.
In an interview with Reuters, Khodorkovsky rejected the accusations - including that the Antiwar Committee had funded and recruited Ukrainian paramilitary units - as "absolutely false".
He said its activity was exclusively public, peaceful and humanitarian.
He said the Council of Europe initiative had touched a raw nerve with Russian President Vladimir Putin because it was bringing together opponents of the Kremlin who, once his rule ends, could one day run the country.
"This alternative point of legitimacy represents the greatest danger for him and his regime," Khodorkovsky said.
"What this shows us is that this very approach to building relationships between international institutions and the consolidated Russian opposition ... is precisely the right approach."
Khodorkovsky, an oil company boss who was once Russia's richest man, served 10 years in a Siberian prison on fraud charges, that he and many foreign governments said were politically motivated, before being pardoned in 2013 and leaving Russia.
Since 2022 he has positioned himself as a leading figure among Russian exiles opposed to Putin.
Shortly after the war's outbreak, he was designated a "foreign agent" by Russia.
Khodorkovsky, who is now based in London, said the latest accusations were a "black mark" from the FSB.
"Without a doubt, such a decision increases the level of risk for those who decide for themselves that they are ready to be an alternative to Putin's regime," he said.
