The former First Lady took to the social media site to congratulate and praise the Swedish activist for her work on climate change. Ms Thunberg previously came under fire after she was named Person of the Year 2019 by Time Magazine.
US President Donald Trump called the accolade “ridiculous”.
But the ex-FLOTUS took to Twitter to defend the activist.
She said: “@GretaThunberg, don’t let anyone dim your light.
“Like the girls I’ve met in Vietnam and all over the world, you have so much to offer us all.
“Ignore the doubters and know that millions of people are cheering you on.”
But Trump took to Twitter to blast Ms Thunberg after the prize was awarded to the 16-year-old.
He said in his post: “So ridiculous. Greta must work on her Anger Management problem, then go to a good old fashioned movie with a friend! Chill Greta, Chill!”
But now Twitter users have taken to the site to express their outrage at Michelle.
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“There’s so much hate with y’all and then you get upset when something is said back! The truth?”
One other user replied: “Too bad Michelle’s lights can’t twinkle out on this controversy.
“Personally I think Thunberg is a viscous snarly spoiled rich kid!”
However, some users defended Michelle and Ms Thunberg.
One user said: “WHAT A DIFFERENCE IN RESPECT AND COURTESY, FROM MICHELLE TO THIS FAKE ONE WE HAVE NOW!!
Another said: “Message to Trump! Will he resist replying and insulting her? Doubt it!”
One user responded: “This is what a true and classy first lady should act like. Take note Melania.
Another user said: “@GretaThunberg The whole world is watching you and the majority if us have your back!! Keep being amazing!”
Before becoming First Lady, Michelle attended Princeton University and Harvard Law School.
She had a career as an attorney at a Chicago Law firm called Sidley & Austin, where she also met her husband Barack Obama.