The region has been a flashpoint for years and tensions there remain high.
Chinese foreign ministry spokesman Zhao Lijian said the alliance risked “severely damaging regional peace… and intensifying the arms race”.
He criticised what he called “the obsolete Cold War… mentality” and warned the three countries were “hurting their own interests”.
And while China was not mentioned directly, the three leaders referred repeatedly to regional security concerns which they said had “grown significantly”.
“This is an historic opportunity for the three nations, with like-minded allies and partners, to protect shared values and promote security and prosperity in the Indo-Pacific region,” a joint statement read.
The Aukus alliance is probably the most significant security arrangement between the three nations since World War Two, analysts say.
It means Australia will become just the seventh nation in the world to operate nuclear-powered submarines.
While they are the big-ticket item in the deal, cyber capabilities and other undersea technologies will also be shared.
Boris Johnson later said the pact would “preserve security and stability around the world” and generate “hundreds of high-skilled jobs”.
In recent years, Beijing has been accused of raising tensions in disputed territories such as the South China Sea.
It has been increasingly assertive over what it says are centuries-old rights to the contested region, and has been rapidly building up its military presence to back up those claims.
The US has bolstered its military presence too, and has been investing heavily in other partnerships in the region such as with Japan and South Korea.
“Beijing has seen over the past months that Australia will not back down and the threats of economic retaliation and pressure simply will not work,” he said.
‘A stab in the back’
But France has also reacted angrily to the new pact, because it means Australia will now abandon a $50bn (€31bn; £27bn) deal with it to build 12 submarines.
“It’s really a stab in the back,” France’s Foreign Minister Jean-Yves Le Drian told France Info radio. “We had established a relationship of trust with Australia, this trust has been betrayed.”
The European Union’s foreign policy chief, Josep Borrell said he understood why France was disappointed by the deal, adding that the EU was not consulted about the new alliance.
“This forces us once again… to reflect on the need to make the issue of European strategic autonomy a priority. This shows that we must survive on our own,” he said on Thursday.
Secretary Blinken said the US cooperated “incredibly closely” with France and would continue to do so, adding that “we place fundamental value on that relationship, on that partnership”.