The magazine depicted Kurdi who drowned on way to Europe would have grown up to be a sexual abuser like those immigrants allegedly involved in the assaults in Cologne in Germany.
More than 500 reported assaults against women on New Year's Eve in Cologne blamed on migrants.
The cartoon was drawn by Laurent Sourisseau, who was in the Charlie Hebdo offices when his colleagues were shot dead by Islamist terrorists in January last year.
The cartoon sparked outcry and many people including prominent journalists condemned the magazine, calling it "disgusting," "racist," and a "disgrace to humanity".
Alan Kurdi made headline in September last year when his lifeless body was found lying face down near a beach in Turkey while trying to reach the Greek island of Kos from the Turkish resort town of Bodrum.
The picture went viral and sparked an international outcry over the human cost of the crisis. Thousands of migrants died last year trying to reach Europe by sea.