Sergei Filin, a 42-year-old former ballet star, was approached by an unknown man who splashed acid on his face as he got out of his car outside his home in central Moscow on Thursday night.
Bolshoi spokeswoman Katerina Novikova, who visited Mr Filin in hospital, said his condition was stable but his eyesight was at risk.
Mr Filin was appointed artistic director of the Bolshoi's ballet company in March 2011.
He danced for the Bolshoi on and off from 1988 to 2004, when he suffered a severe injury on stage.
The theatre's director-general, Anatoly Iksanov, told Russia's Channel One he believes the attack was linked to Mr Filin's work.
Mr Iksanov said: "He was a man of principle and never compromised.
"If he believed that this or that dancer was not ready or was unable to perform this or that part, he would turn them down."
Several stars at the Bolshoi, including Nikolai Tsiskaridze, one of its most celebrated dancers, have complained about what they call Mr Filin's unfair treatment of dancers at the Bolshoi.
Doctors were trying to save his eyesight.