The cover of this week's Maroc Hebdo shows two young men at swimming pool, smiling and gazing into each other's eyes, with the banner headline: "Should We Burn Gays?"
Maroc Hebdo said it "decided to withdraw from sale and its website" this week's edition "given the particularly strong reactions" it caused.
The issue said "homosexuality is, of course, an individual right," but added that debate on the topic had to take into account "moral and religious values".
Homosexuality is illegal in Morocco and can carry up to a three-year jail sentence.
The cover, first circulated on social media, drew instant criticism, with some commentators chiding it as "homophobic", but with its creators saying it was designed to provoke debate.
The magazine said it was not engaging in "sensationalism" but had rather sought to demonstrate "homosexuality and its place in society."
The subject has been in the headlines recently, after Morocco deported two female protesters from the activist group Femen after they staged a topless demonstration criticising Morocco's treatment of homosexuals.
A member of the British rock band Placebo used a festival performance in the capital Rabat last week to also protest Morocco's anti-gay law.
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