The left back has spent the past two seasons with the Pilgrims, and was part of the squad which reached last month's national League North promotion final.
Blackburn-based Duxbury was out of contract this summer but had been discussing terms with the club.
However, he announced his time was up on Twitter.
"Thank you @bostonunited for my time at the club," he wrote.
"Gutted we couldn’t get the promotion over the line. I want wish everyone all the very best for the future.
"Met some great people and friends for life."
Duxbury was labelled a 'warrior' by manager Paul Cox for the way he put himself forward for the play-off semi-final matchday squad at AFC Fylde just days after requiring more than 30 stitches to a facial injury sustained in the eliminator game at Kidderminster Harriers.
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