An elections official said the pro-democracy activist's call for "self-determination" in the Chinese territory was inconsistent with pledging allegiance to the city and its constitution.
If found guilty, the protesters reportedly could face up to 10 years in jail. Demonstrations began several weeks ago over an extradition bill and have grown to include other demands.
"Hello world and hello freedom," said the activist, who served a month on a contempt of court charge. Wong called on Hong Kong's leader to resign after protests over a controversial extradition bill.