The 20-year-old man was arrested at his home in Essendon, in Melbourne's northwest, on Tuesday morning.
Detectives descended on the property to execute a search warrant about 8.30am and later charged him with multiple offences.
Extortion with threats to kill, kidnapping, recruiting a child to engage in criminal activity and false imprisonment were among the charges.
He was also charged with aggravated home invasion with an offensive weapon, common law assault, incitement to commit an indictable offence, among others.
The man, who police previously alleged was a high-ranking representative within a notorious crime syndicate linked to Kazem Hamad, will face court on Tuesday.
Detective Inspector Graham Banks said the man had been in control of tasking crimes out using encrypted applications on behalf of the syndicate.
"Police believe the matters he is being interviewed for (are) the tip of the iceberg," he told reporters following the arrest on Tuesday.
"Despite his young age, intelligence suggests he is a significant part of the crime group."
The accused was known as "Commbank" when using encrypted applications, Det Insp Banks said.
"He came up with this handle based on the amount of wealth he was handling in the organisation," he said.
"I understand he self-described as an ordinary kid who goes to the gym and runs an empire from his home."
There was about 2000 "taskers" at his disposal, Det Insp Banks added, although it could be an elevated number.
Police allege the man was also involved in a kidnapping in the southeast Melbourne suburb of Malvern.
It involved a number of men who assaulted a man inside his home before forcing him inside a car on April 14.
He was later dropped outside a hospital, with police believing the victim was the wrong target.
Four males have been charged over the incident.
Investigators will allege the man had also organised an attempted aggravated home invasion in Doncaster on April 28.
The man is also allegedly behind a number of arson attacks that sparked a major police investigation named Operation Eclipse on April 27.
The operation has been targeting a range of serious and organised crime syndicates believed to be involved in a series of offending linked to hospitality venues, as well as determining the motive for these attacks.
"This arrest is the most consequential we have made since the inception of Operation Eclipse," Det Insp Banks said.
More arrests are expected, with a 23-year-old man also wanted over the attempted murder of Sam ''The Punisher'' Abdulrahim.
He is also allegedly involved in the syndicate and is residing somewhere in the Middle East.
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