The men will be prosecuted in the Hague in a trial scheduled to start on March 9, 2020.
"We now have the information and proof that the Russian Federation is involved in this tragedy, in this crime," Dutch chief prosecutor and JIT coordinator Fred Westerbeke said at a MH17 press conference in Nieuwegein, Netherlands.
Last year, the JIT - which worked in collaboration with the Australian Federal Police - confirmed flight MH17 had been gunned down by a Russian army BUK -M1 missile, which was brought to a field in Pervomaisky, eastern Ukraine from a military base south western Russia.
All three Russians have formal military backgrounds, while Mr Kharchenko of the Ukraine was the leader of a separatist group at the time of the incident.
International arrest warrants have been issued for the men, but none of the four can be extradited per Russian and Ukrainian law which does not permit extradition for criminal trials.
Investigators said the four will be tried in absentia.
Ukraine's prosecutor general Yuriy Lutsenko said the country would try to arrest Kharchenko and, if successful, "fulfill the court sentence" the Sydney Morning Herald reports.
Russian, meanwhile, has vehemently denied any involvement.
Australia's Foreign Minister Marise Payne issued a statement on the charges, saying: "The downing of MH17 was a despicable act and the Australian Government has not stopped in the pursuit of justice for the 298 victims, including 38 Australians."