The rapper took home the hip-hop artist of the year, best collaboration and hustler of the year awards.
Stormzy beat competition from France, South Africe, Brazil, Kenya – and fellow UK rapper Ms Banks – to win best international flow.
The best new hip-hop artist award was given to Pop Smoke, who was shot dead at the age of 20 in February.
When his debut album was released in July, fans told Radio 1 Newsbeat he had “left us something special.”
The BET Hip Hop awards are a spin-off of the main BET Awards which take place in the summer.
The ceremony, which celebrates black entertainment, took place online this year due to coronavirus restrictions.
Megan Thee Stallion’s collaborations with the likes of Cardi B, Nicki Minaj and Ty Dollar $ign have helped shoot her to stardom.
But it was teaming up with BET legend Beyonce – who’s won the most awards in the ceremony’s history – which scored her the win this year, for Savage (Remix).
Beyonce won in another category for the same song – in best featured verse.
Pop Smoke was posthumously honoured with the best new artist award.
The rapper was killed in February after being shot in an apparent armed robbery in LA.
His debut album Shoot For The Stars Aim For The Moon came out in July and went to number one in the UK charts.
Stormzy ‘honoured’ to win
Meanwhile in the best international flow category, Stormzy took home the prize.
“This is my third BET Awards [and] I feel just as honoured as the first time I won it,” he said.
“Know that there’s a whole bag of us from the UK… amazing talent just knocking doors down, smashing it and dropping incredible music.”
The winners in full
Best hip-hop video: Life Is Good by Future ft. Drake
I am hip-hop award: Master P
Hip-hop artist of the year: Megan Thee Stallion
Song of the Year: The Box by Roddy Ricch
Best new hip-hop artist: Pop Smoke
Hip-hop album of the year: Please Excuse Me for Being Antisocial by Roddy Ricch
Best collaboration: Megan Thee Stallion & Beyonce for Savage (Remix)
Best duo or group: Chris Brown and Young Thug
Best Live Performer :Travis Scott
Lyricist of the year: Rapsody
Video director of the year: Teyana “Spike Tee” Taylor
DJ of the year: D-Nice
Producer of the year: Hit-Boy
Hustler of the year: Megan Thee Stallion
Best hip-hop platform: The Joe Budden Podcast
Best featured verse: Beyonce in Savage (Remix)
Impact track: The Bigger Picture by Lil Baby
Best International Flow: Stormzy
Source: The BBC