The decision to return migrants fleeing an earthquake and political instability was “inhumane”, senior diplomat Daniel Foote said in a damning letter.
Last weekend, the US started deportation flights from a Texas border town, where about 13,000 migrants had gathered under a bridge.
They have been waiting in a makeshift camp in temperatures of 37C (99F).
Local officials have struggled to provide them with food and adequate sanitation.
Since Sunday, the US has returned to Haiti 1,401 migrants from the Texas camp on the border with Mexico.
In his resignation letter, Mr Foote said Haiti was a “collapsed state” that “simply cannot support the forced infusion of thousands of returned migrants lacking food, shelter, and money without additional, avoidable human tragedy”.
White House spokeswoman Jen Psaki responded in a press conference: “Special Envoy Foote had ample opportunity to raise concerns about immigration during his tenure. He never once did so.”
Ms Psaki also described images from the border – showing horse-mounted US officers corralling the migrants – as horrific and said horses would no longer be used in the area.
The widely shared pictures, taken by an AFP photographer earlier this week, have evoked grim comparisons to US slavery and the country’s historical mistreatment of black people.
That led to pressure on President Joe Biden’s administration, and prompted calls from within his Democratic Party to give the Haitians asylum rather than fly them back to their home country.
Many Haitians left after a devastating earthquake struck the country in 2010. A large number of those in the camp had been living in Brazil or other South American countries and travelled north after being unable to secure jobs or legal status.
This year has brought further hardship for the impoverished country. In July, President Jovenel Moïse was assassinated – and in August it suffered another deadly earthquake. (Courtesy BBC)