Their eldest child, Usher Raymond V, got stuck in a swimming pool drain at the musician's home.
A court document, filed by Tameka Foster Raymond, says the 5-year-old boy "suffered a near-death accident" while left unsupervised on Monday.
She says Usher has failed to discuss issues affecting the children with her.
He leaves the children with caregivers when he travels around the world for work rather than looking after them himself, she adds.
A lawyer who has previously represented Usher in the custody dispute did not immediately respond to an email seeking comment.
In a statement, Usher has thanked the people who saved his son.
"I am overwhelmed by the outpouring of prayers, love and support for my family's well-being.
"I would like to thank my Aunt Rena as well as the doctors and nurses who are working with us around the clock," he said.
"I would especially like to thank the two men who saved my son's life, Eugene Stachurski and Ben Crews. They are true heroes and I am deeply grateful to them."
Usher and Tameka divorced in 2007 after two years of marriage and fought over custody of their sons; a battle which Usher won.
In court documents she says their sons, aged five and four, would prefer to live with her, rather than the "caregivers" who stay with them while Usher is travelling.
Foster's 11-year-old son, Kile Glover, died last year after he was run over by a jet ski.
At the time Usher appeared on Oprah Winfrey's chat show in the US to talk about the death of his stepson.
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