The country singer scooped the award for her song I Knew You Were Trouble, which was written after the pair's relationship ended after just a few months at the beginning of the year.
"I want to thank the fans because I tweeted about this a lot, I really wanted this," said the 23-year-old after she was presented with her astronaut trophy by Pharrell Williams and Daft Punk.
"I also want to thank the person who inspired this song because he knows exactly who he is, because now I've got one of these", she added, gesturing to the trophy in her hand.
The camera then panned to her ex Harry. The two are believed to have parted ways in February after a holiday to the British Virgin Islands went sour.
Taylor was stunning for her award scoop at the Music Video Awards in Brooklyn, New York, channelling her Hollywood screen siren look in a plunging, body skimming Hervé Leger number.
She sparkled in Lorraine Schwartz jewels, wearing her usually poker straight blonde locks curled into a Twenties hairstyle.
Meanwhile, heartthrob Harry, 19, was looking handsome in an open black shirt, jeans and jacket, his trademark tousled blonde curls perfectly in place.
The British boy band took home an award of their own. One Direction's Best Song Ever also earned its name as the Best Song of the Summer.
The new, entirely fan vote-based category saw the fivesome steal the accolade with nearly 9 million votes.
Miley Cyrus' latest hit We Can't Stop, was in second place with 4.1 million votes, followed by Selena Gomez's Come and Get It, with 2.2 million votes.