Gaga went into the show as the most nominated artist of the evening with 12 nods and she took home four “moon person” trophies taking her career total to 22.
This puts her in third place on the all-time ranking list, ahead of Madonna and behind only Swift and Beyoncé, who have 30 each.
When collecting the award for artist of the year award, she said: “I cannot begin to tell you what this means to me.
“Being an artist is an attempt to connect the souls of people all over the world.”
She left the arena after collecting the award, but the MTV cameras later followed her across the city to her live concert at Madison Square Garden where she performed Abracadabra and The Dead Dance.
Tim Burton directed the gothic music video to the latter song which also appeared on the soundtrack to the new Netflix Addams Family show, Wednesday, in which Gaga also makes a guest appearance.
She also won awards for best direction and art direction for Abracadabra, as well as best collaboration for her song Die With A Smile alongside Bruno Mars.
Another Mars collaboration, his song APT with Rosé, won song of the year while the South Korean singer’s outfit Blackpink were named best group.
“This is a really big moment for 16-year-old me and anyone else who has dreamed about being accepted equally for their hard work,” said an emotional Rosé during a lengthy speech.