A foreign ministry spokesman called the comments unacceptable, and the official Communist Party newspaper described the criticism as “super arrogant”.
Mrs Clinton on Friday called China and Russia’s veto of a UN resolution on Syria “despicable”.
The Chinese criticism came a day after Syria held a national referendum on a new constitution, amid violent unrest.
The referendum calls for a multi-party parliamentary election within three months. The opposition has dismissed Sunday’s vote as a farce, as at least 30 more deaths were reported around the country.
Ms Clinton made her remarks at the Friends of Syria conference in Tunisia, a meeting of diplomats boycotted by China and Russia that sought an end to the crisis.
The US Secretary of State said it was “quite distressing” to see two Security Council members using their vetoes “while people are being murdered”.
“It is just despicable and I ask whose side are they on? They are clearly not on the side of the Syrian people.”
Foreign Ministry spokesman Hong Lei, when asked for Beijing’s response, said China “cannot accept that at all”, AFP news agency reported.
Communist Party mouthpiece the People’s Daily was more outspoken.
“The United States’ motive in parading as a ‘protector’ of the Arab peoples is not difficult to imagine,” it said in a commentary. “The problem is, what moral basis does it have for this patronizing and egotistical super-arrogance and self-confidence?”
“Even now, violence continues unabated in Iraq and ordinary people enjoy no security. This alone is enough for us to draw a huge question mark over the sincerity and efficacy of US policy,” it added.
While China is traditionally resistant to interference in other countries’ affairs, it has come under intense pressure on Syria.
Beijing believes that Syrian leader Bashar Al-Assad should be allowed to carry out reforms to try and end the bloodshed, says the BBC’s Martin Patience in Beijing.
But observers say the power to end the violence lies with Beijing and Moscow, which have so far provided the diplomatic support that has shielded Syria.
On 4 February they blocked a resolution in the UN Security Council backing an Arab plan condemning the crackdown and calling on Mr Assad to step down.