The Thiruvananthapuram Lok Sabha member launched the drive at the Kovalam beach.
"Before my actions today are distorted: a clean India requires no label. Why cede Gandhiji's sanitation drive to any party? A national cause," he tweeted later.
Tharoor and a few other Congress workers and representatives of local bodies held brooms and took to the job of cleaning streets.
"I am a Congressman and my ideology is there should be clean surroundings. I first arrived in this city when I was 10 years and at that time even after heavy rains, the city used to be clean due to the excellent drainage facility. But today, urban planning has failed and the place here has become like a sewage dump," said Tharoor.
Tharoor said it was Mahatma Gandhi who said sanitation is more important than independence.
"Cleanliness is a national programme... not the programme of any particular party," he added.
Prime Minister Narendra Modi had nominated Tharoor to spread the message of a clean India.