"The hatred that struck us is still there and, since 2015, it has taken the time to mutate, to change its appearance, to go unnoticed and to quietly continue its ruthless crusade," he said.
Twelve people, including some of France's most celebrated cartoonists, were killed on 7 January, 2015, when brothers Said and Cherif Kouachi went on a gun rampage at the paper's offices in Paris.
The perpetrators were killed in the wake of the massacre but 14 alleged accomplices in the attacks, which also targeted a Jewish supermarket, will go on trial in Paris on Wednesday.
The latest Charlie Hebdo cover shows a dozen cartoons first published by the Danish daily Jyllands-Posten in 2005 - and then reprinted by the French weekly in 2006, unleashing a storm of anger across the Muslim world.
In the centre of the cover is a cartoon of the prophet drawn by cartoonist Jean Cabut, known as Cabu, who lost his life in the massacre.
"All of this, just for that," the front-page headline says.
The issue will be available from French newsstands just as the trial gets underway on Wednesday morning and can already be read by subscribers online.
'The right to blaspheme'
The editorial team wrote that now was the right time to republish the cartoons and "essential" as the trial opens.
"We have often been asked since January 2015 to print other caricatures of Mohammad," it said.
"We have always refused to do so, not because it is prohibited - the law allows us to do so - but because there was a need for a good reason to do it, a reason which has meaning and which brings something to the debate."
The paper's willingness to cause offence over a range of controversial issues has made it a champion of free speech for many in France, while others argue it has crossed a line too often.
But the massacre united the country in grief, with the slogan #JeSuisCharlie (I Am Charlie) going viral.
"A thousand bravos," Zineb El Rhazoui, a former journalist for the weekly, said on Twitter, calling the republication of the cartoons a victory "for the right to blasphemy".
The former director of Charlie Hebdo, Philippe Val, also hailed a "remarkable idea" for defending freedom of thought and expression in the face of "terror".
In a nuanced response, the president of the French Council of Muslim Worship (CFCM), Mohammed Moussaoui, urged people to "ignore" the cartoons, while condemning violence.
"The freedom to caricature is guaranteed for all, the freedom to love or not to love (the caricatures) as well. Nothing can justify violence," he told AFP.
The renewed debate also comes after the ultra-conservative weekly Valeurs Actuelles faces a probe by prosecutors and accusations of crossing the line after depicting a black MP as a slave with an iron collar round her neck.
'Not little helpers'
The suspects, who go on trial on Wednesday morning, are accused of providing various degrees of logistical support to the killers.
The trial had been delayed several months with most French courtrooms closed over the coronavirus epidemic.
The court in Paris will sit until 10 November and, in a first for a terror trial, proceedings will be filmed for archival purposes given public interest.
National anti-terror prosecutor Jean-Francois Ricard dismissed the idea that it was just "little helpers" going on trial since the three gunmen were now dead.
"It is about individuals who are involved in the logistics, the preparation of the events, who provided means of financing, operational material, weapons, a residence," he told France Info radio on Monday.