Ms Chhillar on Saturday won the title in China, ending 16 years of drought for India at the international beauty pageant.
Referring to her, Mr Tharoor tweeted: "What a mistake to demonetise our currency! BJP should have realised that Indian cash dominates the globe: look, even our Chhillar has become Miss World."
This didn't go down well with many.
One Twitter user wrote: "Shame on you Mr. Tharoor. You are the one who disrespected Haryanvi surname 'Chhillar' and linked it with a joke."
Another tweeted: "This is not funny at all. Making fun of someone's surname is not what we expect from you...disheartened."
Mr Tharoor soon took to Twitter and Facebook to ask people to chill.
"Guess the pun is the lowest form of humour, and the bilingual pun lower still! Apologies to the many who seem to have been righteously offended by a light-hearted tweet today. Certainly no offence was meant to a bright young girl whose answer I've separately praised. Please: Chill!"