The judge, Andrew S. Hanen of the Federal District Court in Houston, said the program, known as Deferred Action for Childhood Arrivals, had been relied upon by hundreds of thousands of immigrants since it was established almost six years ago, and should not be abruptly ended.

The Texas judge, who in 2015 blocked a similar effort by Mr. Obama that would have added protections for the undocumented parents of citizens and other lawful residents, compared the idea of ending the DACA program to an attempt to “unscramble” an egg.

“Here, the egg has been scrambled,” Judge Hanen wrote. “To try to put it back in the shell with only a preliminary injunction record, and perhaps at great risk to many, does not make sense nor serve the best interests of this country.”

“The reality of the situation is that it conferred lawful presence and numerous other benefits, and many DACA recipients and others nationwide have relied upon it for the last six years,” Judge Hanen wrote.

He also added that “DACA is a popular program and one that Congress should consider saving.”