Rowghani joined Twitter in March 2010 after nine years with Pixar Animation Studios, where he served as the CFO and Senior Vice President of Strategic Planning for Pixar Animation Studios, Disney Animation Studios, and Disney Toon Studios.
He will, however, continue to be an employee at Twitter acting as a strategic advisor to the CEO Dick Costolo.
"Effective today, Ali Rowghani has resigned from his position as the COO of Twitter," the company said.
Twitter does not intend to hire a replacement for the COO role, and all of Rowghani's operating responsibilities will be assumed by other members of the Twitter management team.
In a tweet, Rowghani said: "Goodbye Twitter. It's been an amazing ride, and I will cherish the memories."
Prior to Pixar, Ali was an associate at consulting firm McKinsey & Company.
Ali holds a Bachelor of Arts degree and a Master of Business Administration degree, both from Stanford University. He was awarded a Fulbright scholarship and spent a year studying at the University of Bonn in Germany.
The San Francisco-based social media company has been trying to increase its user base, especially in emerging countries like India.
It also aims to drive traffic using popular events like elections and FIFA World Cup, allowing fans to follow teams and players using its service.
Twitter claims to have 255 million monthly active users with 500 million tweets sent every day. About 78 per cent of its active users are on mobile and 77 per cent of accounts are outside the US. It supports over 35 languages.