The Indigenous senator said she wanted to represent the "strong, grassroots, Black sovereign movement full of staunch and committed warriors".
"It has become clear to me I can't do that from within the Greens," she told reporters in Canberra on Monday, the first day of parliament for the year.
Senator Thorpe said her new independence would enable her to better fight for First Nations justice and sovereignty.
"I'm ready for what comes next in the fight for a future where our kids are with their families, where our people are not killed in custody, where the chains that the system wraps around our people are lifted," she said.
Senator Thorpe said a voice to parliament was at odds with what her community had told her but noted she had not reached her final position on the constitutional change, which is expected to be put to a referendum later this year.
Greens leader Adam Bandt told reporters he would have liked Senator Thorpe to stay in the party but respected her decision.
"I confirmed that, under the Greens' constitution, she had the ability to vote differently," he told reporters in Canberra in relation to the voice.
The minor party is expected to come to a decision on the voice within days.
Senator Thorpe has said she would not support the voice unless there was a guarantee that Indigenous sovereignty would not be ceded.
Prime Minister Anthony Albanese, constitutional experts and the referendum working group have said the voice would have no impact on First Nations sovereignty.
Mr Bandt said he and a lot of party members and voters were saddened by the outcome when asked whether Victorian voters had been sold a pup for voting for someone they thought would remain in the Greens.
"She's made that decision and she's explained her reasons for doing it. And we just have to deal with the facts as we find them," he said.
Her announcement means the Greens will be reduced from 12 senators to 11 and the government will have an additional independent crossbencher to negotiate with.
She will continue to vote with the Greens on climate issues in the Senate.
Crossbencher Jacqui Lambie said it "took guts" and being independent was the best way to represent your community.
"No party lines, no talking points," the Tasmanian senator tweeted.
"Every time the cross bench grows, it's a good thing. Representation gets more representative. Love to see it."
One Nation leader Pauline Hanson attacked the Greens for having an "identity crisis" and that the defection was an indictment on Mr Bandt.
The Queensland senator also called on the prime minister to reject negotiating with Senator Thorpe to pass legislation due to her "black nationalist extremism".
Senator Thorpe replaced former Greens leader Richard Di Natale when he retired in 2020 and was re-elected in 2022.