Beijing said he was under investigation by the country's anti-corruption body for unspecified breaches of the law.
Mr Meng, also a vice-minister of public security in China, was reported missing after travelling from the city of Lyon in France, where Interpol is based, to China on 25 September.
Interpol said it had received his resignation from the presidency on Sunday with immediate effect.
Meanwhile Mr Meng's wife, Grace Meng, has told reporters that her husband sent her a knife emoji in a social media message on the day he went missing.
She said her husband's case would be under the scrutiny of "international law and international public opinion".
On Monday, after days of speculation about Mr Meng's whereabouts, China's National Supervision Commission said in a statement that he was under investigation.
The commission handles corruption cases involving public servants.