The aid agency said the new runway was a "massive step backwards" in the battle against climate change "that will have repercussions far beyond Britain's shores".
Christian Aid's senior climate change adviser Dr Alison Doig said it was "imperative" that world leaders reach a new deal on climate change when they meet for a major UN summit in Copenhagen in December.
"One of the thorniest issues in the negotiations will be demands from the industrialised world that developing countries must cut their emissions. Poorer countries argue that they have little responsibility for global warming, and it is up to richer countries to put their own houses in order first," she said.
"A great deal of mistrust exists on both sides. The building of a third runway at Heathrow will be seen by many in the developing world as evidence that rich countries will always put self interest above any real desire to tackle climate change."
Christian Aid warned that the Government was in danger of failing to meet its target of reducing carbon emissions in the UK by 80 per cent by 2050, unless it offsets the UK's carbon emissions by paying poorer countries to limit their emissions.
Ms Doig said a third runway at Heathrow would not solve the airport's congestion problem.
"The simple truth is, despite the rhetoric, the UK is set to produce more emissions, not less. Those in favour of the runway say it will reduce congestion in the skies above London, and so reduce emissions," she said.
"One only has to look at the M25, which was also built to reduce congestion, to see just how much more traffic such developments generate."
Christian Aid is urging the Government not to offset its carbon emissions abroad but instead make even bigger emissions cuts at home.
"To keep climate change in check, we should make real cuts in emissions domestically reaching our own targets at home, and additionally support poor countries to develop in a low-carbon way," she said.
Christian Aid is also calling on the Government to abandon plans for a new coal-fired power plant at Kingsnorth. The plant, it warns, will emit in excess of seven million tonnes of carbon emissions a year, equivalent to more than the annual emissions of 30 developing countries combined.
She said: "The next climate challenge for the UK government will be the decision as to whether or not to go ahead with Kingsnorth, which will emit as many greenhouse gases as 30 of the world's poorest countries combined. The Heathrow decision makes it even more critical that that project does not get the go-ahead."