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The U's sit 19th in League One, following a run of one win in nine. United's last match saw them defeated 3-2 at home to bottom side Crewe Alexandra, despite going 2-0 up.
Humes replaced Joe Dunne in September 2014, and leaves with the club sporting the worst defensive record in the Football League.
Assistant manager Richard Hall, current under-21s boss John McGreal will take charge of Saturday's game at Burton Albion.
Humes record at Colchester:
Wins | Draws | Defeats |
---|---|---|
22 | 14 | 31 |