Some 179 people were arrested across Europe and the US, and 500kg (1,102lb) of drugs and 64 guns confiscated.
It ends the "golden age" of these underground marketplaces, Europol said.
"The hidden internet is no longer hidden", said Edvardas Sileris, head of Europol's cyber-crime centre.
The operation, known as DisrupTor, was a joint effort between the Department of Justice and Europol. It is believed that the criminals engaged in tens of thousands of sales of illicit goods and services across the US and Europe.
Drugs seized including fentanyl, oxycodone, methamphetamine, heroin, cocaine, ecstasy and MDMA.
Of those arrested 119 were based in the US, two in Canada, 42 in Germany, eight in the Netherlands, four in the UK, three in Austria and one in Sweden.
Police are getting better at targeting operations on the dark web - a part of the internet that is accessible only through specialised tools. This latest raid follows the takedown of the Wall Street market last year, which was then thought to be the second-largest illegal online market on the dark web.
Mr Sileris said: "Law enforcement is most effective when working together, and today's announcement sends a strong message to criminals selling or buying illicit goods on the dark web: the hidden internet is no longer hidden and your anonymous activity is not anonymous."
"With the spike in opioid-related overdose deaths during the Covid-19 pandemic, we recognise that today's announcement is important and timely," said FBI director Christopher Wray.
Kacey Clark, a researcher at dark web monitoring specialist Digital Shadows said: "This is another further blow to organised cybercrime. The operation which took down the AlphaBay and Hansa marketplaces three years ago spooked cyber criminals, since it resulted in many follow up prosecutions as law enforcement pieced evidence together - often many months later.
"Wall Street market emerged from these ashes and was the most significant one in existence at the time. It would appear that law enforcement has followed the same pattern and that is why we are seeing arrests today."