The 25-year-old had been with Silkmen since 2013 after starting his career at Stockport County.
He was captain of the Macclesfield side that lost at Wembley in the FA Trophy final this season to York City.
Halls is Chester's third close-season signing, after the arrival of strikers Harry White and Nyal Bell.
White was signed from Solihull Moors, while Nyal Bell has joined on a half-season loan from Gateshead until 7 January.
Jon McCarthy's side finished 19th in the table, narrowly avoiding relegation, having been seventh at Christmas.
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Chester have signed full-back Andy Halls on a one-year deal after he turned down a new contract with fellow National League side Macclesfield Town.