He said they are donating their fortune to the Chan Zuckerberg Initiative because they want to make the world a better place for Max to grow up in.
Mr Zuckerberg said the donation currently amounts to $45bn (£30bn).
Max was born last week, but the couple only made the news of her birth public on Tuesday.
In his letter Mr Zuckerberg said the aim of the Chan Zuckerberg Initiative is "to advance human potential and promote equality for all children in the next generation".
Its initial areas of focus will be personalised learning, curing disease, connecting people and building strong communities.
"Your mother and I don`t yet have the words to describe the hope you give us for the future," Mr Zuckerberg said at the start of his letter to Max.
"You`ve already given us a reason to reflect on the world we hope you live in," it added.
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