The shooting happened around 6:30 p.m. Sunday in the 11900 block of Madera Run Parkway near Timber Forest in Atascocita.
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Investigators said the deputy had just picked up dinner for his family and was driving along Madera Run when the shots were fired.
Harris County Pct. 3 Constable Sherman Eagleton identified the deputy killed as 37-year-old Omar Ursin.
A black or dark-colored four-door sedan with tinted windows pulled up beside the deputy and fired shots into the driver's side of his car, officials said.
"The reason for the shooting at this point is unknown," Sgt. Dennis Wolfford said. "We don't know if it was road rage. We don't know if it has something to do with him being law enforcement. We're still trying to determine that."
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After the shooting, Ursin crashed into a tree in the median, deputies said. He was transported to an area hospital, where he later died.
The suspect's car reportedly turned north on Olympic National Drive, investigators said. It has not been located.
Investigators are asking anyone with information or surveillance video to contact HCSO at 713-221-6000.