More than 10 weeks of sometimes-violent demonstrations have wracked the semi-autonomous city, with millions taking to the streets to demand democratic reforms and police accountability.
Over the past week the airline has emerged as a target on the mainland after some of its 27,000-strong workforce took part in, or voiced support for, the protests.
China's aviation regulator demanded that the airline prevent such staff from working on flights to the mainland or those routed through Chinese airspace.
It also ordered the carrier to hand over identity information for employees on mainland-bound flights -- declaring unapproved flights would not be allowed in.
Executives scrambled to reassure authorities that the company has no truck with the demonstrators, vowing to sack any employee who takes part in an "illegal protest".
It has since fired two employees, suspended a pilot linked to the demonstrations and said it will comply with China's regulators.
But the move was not enough to avoid the crosshairs of China's staunchly nationalist Global Times tabloid and the People's Daily -- the Communist Party's mouthpiece.
Cathay's "sins", the papers said, were that it had not done enough to investigate or condemn staff who took part in protests.
Fired up by the thunderous state media articles, China's heavily censored social media platforms lit up with indignation from people vowing never to fly Cathay again.
On China's Twitter-like Weibo platform, the hashtag #boycottcathaypacificairline had racked up nearly 45 million views by Wednesday.
"Blacklist this airline from now on," wrote one user.
A protester blockade of the airport this week deepened the airline's woes, forcing it to cancel 272 flights, and affecting the travel plans of 55,000 people, it said.
Analysts said Cathay is acutely vulnerable to any potential censure from Beijing.
"They are so heavily reliant on the mainland Chinese market," noted Brendan Sobie, chief analyst for the Centre for Aviation.
He said a fifth of the company's flights are to, or from, the mainland while Chinese passengers make up some 80 percent of passengers on flights to other markets.
The pressure sent Cathay's shares into a nosedive, losing nearly five percent at the start of the week.
The company has swung into damage limitation mode.
Swire Pacific -- a Hong Kong-based conglomerate and Cathay's largest shareholder -- released a statement saying it "strongly supports" the Hong Kong government and "(shares) the vision of the Chinese Central government".
"We resolutely support the Hong Kong SAR Government, the Chief Executive and the Police in their efforts to restore law and order," the company said, adding that it would comply with any regulations Beijing placed on it.
Cathay released a similarly worded statement on Wednesday.
"We firmly believe that social order and stability must be restored in Hong Kong so that the long-term development and prosperity of our city can again become our priority," it said.
But while Cathay's moves may be intended as balm for Beijing's anger, the airline has hardly endeared itself to the protest movement, which enjoys a measure of support among the seven million people who call Hong Kong home.
One cartoon that summed up protester sentiment and quickly went viral was drawn by Australia-based Chinese dissident artist Badiucao.
In it he renamed the airline Cathay Pathetic -- the opening C turned into a communist hammer and sickle.
Some of those inside the company now say a climate of fear has descended with many worried their own colleagues may be spying on each other's political views.
"It feels like you're being silenced. You can't even express your support on social media," a flight attendant who gave her name as Cat told AFP this week.
"And many colleagues are actually pointing people out, saying they might send lists to the company about who supports these illegal protests. That makes everyone really afraid," she added.