Canadian Lanez, 28, is alleged to have shot the rising hip-hop star following an argument in the Hollywood Hills on July 12.
Prosecutors said he shot at her feet, wounding the 25-year-old and leaving her needing surgery.
Lanez has been charged with one felony count each of assault with a semi-automatic firearm and carrying a loaded, unregistered firearm in a vehicle.
He also faces a gun allegation and that he personally inflicted great bodily injury, the Los Angeles County District Attorney’s Office said.
Lanez, whose real name is Daystar Peterson, did not appear at an arraignment hearing in Los Angeles on Tuesday and participated in the brief court session over the phone.
His solicitor, Shawn Holley, did not enter a plea on his behalf.
Judge Miguel Espinoza deferred the arraignment to November 18 and granted a request for a protective order for Megan Thee Stallion.
Lanez was ordered to stay at least 100 yards away from the musician, have no contact with her and told to sell any guns in his possession or submit them to authorities within 24 hours.
He posted his 190,000 dollar bail (about £146,000) during the hearing at the Clara Shortridge Foltz Criminal Justice Centre.
In music released last month, Lanez denied shooting Megan Thee Stallion, whose real name is Megan Pete, and suggested he had been framed.
Megan Thee Stallion is one of the brightest rising stars in rap music. Following weeks of speculation, she directly accused Lanez of shooting her in August, saying in an Instagram live video: “Yes … Tory shot me. You shot me and you got your publicist and people to these blogs lying. Stop lying!”
She had shared earlier videos, breaking down while telling fans she had to undergo surgery to have bullets removed from her feet.
Megan Thee Stallion described the alleged shooting as “the worst experience of my life” but said she felt fortunate not to be more seriously hurt.
The Houston-born rapper has enjoyed a hugely successful 12 months. Her single Savage was an international hit, reaching number three in the UK charts, with Beyonce later featuring on a remix.
Time magazine named Megan Thee Stallion one of the 100 most influential people in the world.
