Countries have jurisdiction in criminal matters primarily because either (1) the crime affects people in their country, or (2) the crime is carried out in their country.
The Netherlands is well within established norms of criminal jurisdiction to enforce money laundering laws that impact commerce in or with the Netherlands, which appears to be what happened in this case.
Also, the locus of where a crime that takes place on the Internet occurs is also somewhat nebulous. If Dutch residents are parties to those transactions, and the transactions constitute money laundering under Dutch law, there is a fair argument that the money laundering transactions take place in the Netherlands for legal purposes.
The main issue, as a practical matter, is what the Netherlands can do in order to force Binance to comply with its orders if Binance fails to do so.
The political and legal reality is that as long as the Dutch courts have the practical ability to enforce their orders, the Netherlands has jurisdiction to enforce those orders from a legal perspective if the Dutch courts agree that they have the power to do so.
I lack the technical level understanding of the operations of Binance to know precisely what the Dutch government could do in this case, however. Someone with a deeper technical understanding will have to address that issue. It could simply be that the Dutch government is confident that it could successfully extradite Binance officials who willfully disobeyed its orders from whatever countries they reside in.
Usually extradition is available, if there is an extradition treaty in force, if both countries have laws criminalizing the same basic type of conduct with similar degrees of seriousness. So, if the country where the Binance officials are located has a money laundering law that is in broad outline similar to that of the Dutch money laundering law, and if the two countries have an extradition treaty, the Dutch threat to have the offenders outside the Netherlands arrested and extradited to the Netherlands is a credible one.
According to Wikipedia:
Binance is a cryptocurrency exchange which is the largest exchange in the world in terms of daily trading volume of cryptocurrencies. It
was founded in 2017 and is registered in the Cayman Islands.
Binance was founded by Changpeng Zhao, a developer who had previously
created high frequency trading software. Binance was initially based
in China, but later moved its headquarters out of China following the
Chinese government's increasing regulation of cryptocurrency.
In 2021, Binance was put under investigation by both the United States
Department of Justice and Internal Revenue Service on allegations of
money laundering and tax offenses. The UK's Financial Conduct
Authority ordered Binance to stop all regulated activity in the United
Kingdom in June 2021.
Japan, Thailand, and Malta (another E.U. member) are also involved in enforcement efforts against Binance.
Under the circumstances, it looks like the Netherlands would probably have the U.S., the U.K., E.U., Japanese, and Thai money laundering officials on its side, so it could expect considerable cooperation in its international efforts to enforce it orders.
While officially organized in the Cayman Islands (a notorious tax and asset protection haven), it appears that the brain trust of the organization is based in China, which might not be so cooperative. But, multinational business executives can be greatly hampered if warrants for their arrest are outstanding in much of the world.
Also, China, while it is prone to ignore business corruption for extended periods of time, every now and then embarks on harsh, mass, anti-corruption campaigns in which large numbers of allegedly corrupt business people are executed or imprisoned with little or no formal due process in short order and with little warning. So, Chinese based executives of the company know that if they become too much of a problem to the Chinese government and the Communist Party of China, that they can be "thrown under the bus" in a manner much more literal than the way that this term is usually used. Chinese billionaires have short life expectancies.