Kate, 35, recently hinted she'd like a third child after being handed a gift designed for newborns during the couple's royal tour of Poland and Germany.
She was seen turning to William at the business event in Warsaw and saying: "We will just have to have more babies."
The organisation said that Kate's comments raised "compelling issues of sustainability and equity".
Having Kids executive director Anne Green said: "William and Kate have a tremendous opportunity to model their choice of having a smaller family.
"By doing so, they set an example as to what has the most potential for mitigating climate change and its impacts, including severe flooding, deadlier heatwaves, increase in diseases, and wildlife extinctions."
She added: "Moreover, given the vast economic inequalities in the world today, the couple also has the opportunity to model a simple principle: That every child deserves as fair start in life".
But the organisation's open letter has been met with some scepticism, with one woman writing on Facebook: 'This is beyond the most ridiculous thing I have ever read.
"If someone wrote a letter to me suggesting how many children I should have, regardless of my societal status, I'd be sure to kindly return the letter, straight into their a**. Although there may not be enough room since their head is already so far up their a**."
On its website, the San Francisco-based organisation says its mission is to promote and protect "every child's right to a fair start in life by replacing parent-centered family planning models with the child-centered Fair Start family planning model."
A third child for the Duke and Duchess of Cambridge would mean a little brother or sister for Prince George, four and two-year old Princess Charlotte - currently third and fourth in line to the throne.
MailOnline has contacted Having Kids for further information.
