The first cartoon shows a clown and what appears to be the toddler with a sign: "Welcome immigrants, so close to his goal. Promotion: Two children for the price of one."
The second cartoon, "Proof that Christians walk on water" shows a man supposedly resembling Jesus walking on water as a partially submerged child says "Muslim children drown."
Heart-rending photos of the toddler's lifeless body washed ashore on a Turkish beach last week sparked global horror and debate on refugees.
The magazine's cartoons sparked outrage on social media, Al Jazeera reported.
Peter Herbert, chair of the Society of Black Lawyers, tweeted that the group would consider reporting Charlie Hebdo's actions as "an incitement to hate crime & persecution before the International Criminal Court".
In January, armed men who identified as being members of al-Qaeda stormed the magazine's Paris offices, killing 11 people in the building and injuring another 11.
The magazine had published images mocking Prophet Muhammad.
A manhunt ensued and several related attacks followed in the Île-de-France region, where a further five people were killed and 11 wounded.