Cyrus performed with Thicke on his track 'Blurred lines' and was seen twerking and flirting with the singer on stage at MTV Video Music Awards.
Bhatt, 41, took to Twitter to speak in favour of Cyrus.
"Bash Miley Cyrus yet say nothing about Robin Thicke and his obnoxious lyrics. How can the world be different from our own backyards," she tweeted.
"So she twerked, stuck out her tongue, pissed the world off. Cannot take away from the fact that the girl can sing and 'We can't stop' rocks!"
The award ceremony took place at the Barclays Center in Brooklyn on August 25. Cyrus has been making headlines since then for her racy performance with Thicke.
Photos: Katrina Kaif, Shamita Shetty at Mumbai airport
Photos: Varun Dhawan, Alia Bhatt promote 'Badri...' on 'Dil Hai Hindustani'
In pictures: 15 facts about kissing that will surprise you
Photos: Shahid Kapoor and Mira Rajput at cafe in Bandra
Photos: Deepika Padukone, Neha Dhupia and Soha Ali Khan at event