The new charges against the former prime minister include anti-terrorism offences, multiple sections of its criminal code, Dawn newspaper reported.
The charges have been filed by the Lahore city police against 70-year-old Mr Khan and around 2,000 workers and supporters of his Pakistan Tehreek-i-Insaf (PTI) party.
They include attempt to murder, punishment for abetment, criminal conspiracy, armed rioting, criminal intimidation, obstructing public servants, causing public nuisance, mischief by fire or explosive substance with an intent to damage public property, among others.
It came as a court suspended an arrest warrant against Mr Khan, giving him a reprieve to travel to Islamabad and face charges in a fraud case brought by his rival and successor.
Khan has been holed up at his home since Tuesday, after failing to appear at an earlier hearing in the case. His supporters hurled stones and clashed with baton-wielding police for two days to protect the former premier from arrest.
Khan, now in the opposition, was ousted in a no-confidence vote in Parliament last April. He is accused of selling state gifts while in office and concealing assets. It's one of a string of cases that the former cricket star turned Islamist politician is facing since his ouster.
Mr Khan’s supporters have barricaded his home as the court is expected to decide whether the cricketer-turned-politician is to be arrested or not.
The fresh charges were filed on the basis of a complaint of police inspector Rehan Anwar who alleged PTI workers committed terrorism at the behest of the former prime minister.
He also alleged that violent riots were orchestrated by a criminal conspiracy led by Mr Khan.
Usman Anwar, an Inspector General of Police from the Punjab province, said personnel had demonstrated restraint at Mr Khan’s residence in the upscale Zaman Park neighbourhood to “avoid the loss of lives”.
He also denied allegations that the police used weapons during the standoff and claimed Islamabad and Lahore police had not fired a single shot at PTI workers.
On Tuesday, violent scenes were witnessed at his home, as around 1,000 supporters of Mr Khan clashed with the police who were attempting to arrest the former prime minister.
Mr Khan’s supporters hurled petrol bombs, rocks and bricks at the police. Officers responded by swinging batons, firing teargas and using water cannons at scores of supporters.
The officers failed to arrest Mr Khan and the Lahore court had on Thursday extended a stay on police operations to take him into custody.
Mr Anwar said police would comply with the court’s orders and seek his custody again on Friday.
Mr Khan has also been barred by the court from holding a rally on Sunday ahead of assembly elections in Punjab, of which Lahore is the provincial capital.
Mr Khan, who was ousted in a no-confidence vote in parliament in April last year, was ordered to appear before a judge in Islamabad last Saturday to answer charges of illegally selling state gifts he had received during his term as premier and concealing his assets in what is known as the Toshakhana case.
Mr Khan has blamed his successor, prime minister Shehbaz Sharif, for his ouster and called it a “conspiracy” formed with the US. Both the US and Pakistan governments have denied his allegations.