In the photo an immaculately made-up and bejeweled Melania Trump, 46, poses before a bowl of glittering baubles, twirling a sparkling silver chain with her fork as if it were pasta.
The cover has infuriated many Mexicans, coming in a week that saw the nations plunge into the biggest diplomatic crisis in decades.
Trump has insisted Mexico pay for his planned border wall, which Mexican President Enrique Pena Nieto has said will never happen.
The dispute prompted Pena Nieto to scrap a meeting with Trump in Washington that had been scheduled for next week, while the White House raised the possibility of slapping tariffs on Mexico to fund the wall
Many social media users have called the Vanity Fair cover "humiliating" and in "bad taste" considering President Trump's criticism of Mexico.
"Thank you @VanityFairMX for putting Melania Trump on the cover. Great example of sensitivity, empathy, patriotism and editorial intelligence," tweeted Denise Dresser, a well-known Mexican intellectual.
"We understand the complicated moment that has coincided with the appearance of our cover," Vanity Fair Mexico said in a statement published on its website following the initial backlash.
"But our intention is simply to contribute, as always, an independent and critical point of view about current affairs and the characters involved."
The recycled interview and photo originally appeared in GQ's April 2016 issue. That magazine and Vanity Fair are owned by the same parent company, Conde Nast.
Vanity Fair Mexico features an article about the US First Lady Melania Trump. Source: AAP
In December the new American president blasted the US edition of Vanity Fair after the magazine published a snooty review of one of his restaurants.
Following the Republican's twitter barb the magazine's subscription numbers broke a company record.
The Mexican edition of Vanity Fair sparked past controversy after featuring actress Angelica Rivera, the Mexican president's wife, who has faced corruption allegations.
