Receiving a massive 60 percent of the public votes, Harry managed to see off Adele, Ed Sheeran and Foo Fighters to win the prestigious prize.
Other acts short-listed for the award included Stormzy, Iron Maiden and singer Dua Lipa.
It's the first time Harry has won it as a solo artist, but his old band One Direction twice scooped The Silver Clef Awards.
The Silver Clef Awards, which is an annual UK music awards that has been running since 1976, sets out to "recognise excellence in music" with the ceremony itself helping to raise money for music therapy charity Nordoff Robbins.
The charity’s chief executive, Julie Whelan, said: "The O2 Silver Clef Awards are one of the reasons why Nordoff Robbins is able to continue delivering life-changing music therapy to so many people facing some of the biggest challenges who desperately need our help.
"For 43 years this event has celebrated the best names in music, whilst raising over £10.5m for our charity to date. We are forever grateful for the tremendous support it receives year on year."
The award tops off a great 12 months for Harry, who is in the middle of his first major global tour as a solo artist. He must be still feeling on top of the world after self-titled album and single Sign Of The Times topped the UK charts last year.
The winners of the other categories were already announced earlier. Roger Waters will be honoured with the Silver Clef Award that is presented for outstanding contribution to music.
Led Zeppelin’s Robert Plant is the recipient of the outstanding award, and this year’s icon award has been won by the Stereophonics.
Our own The Script have won the international award.