A 2-1 defeat at the Shay left them four points clear of the relegation zone but they had not won in six league matches, writes Tom Feaheny.
A club statement said.
"Following last night's defeat to Leyton Orient it has been mutually agreed, that FC Halifax Town and manager Billy Heath will part company.
"The decision has not been taken lightly. The Board would like to place on record their sincere gratitude to Billy for achieving promotion at the end of the 2016-17 campaign.
"Billy leaves with our very best wishes for the future."
Heath last night after the defeat had made it clear that his players were giving it their all.
"The players are desperately trying to get three point, they are putting a shift in each time. They’re giving everything they can, but we’re just lacking a bit of quality at times.”
“We've conceded goals that were avoidable at key times, where a player had made a wrong choice.”