Emile Sinclair struck in each half to earn the Silkmen a shock first-round win in front of a crowd of 4,826, the lowest ever at the KC Stadium.
Pearson, whose side were jeered off at the final whistle, told the Hull Daily Mail: "To be beaten at this stage again by a lower league side is clearly not good enough.
"It was a poor performance, it wasn't good enough. There's certainly a few alarm bells ringing, there's no doubt about that.
"We've not shown enough quality and at times not shown enough desire. That's very disappointing."
Hull, who went down 1-0 at home to Blackpool in their opening league game last Friday, were without nine first-team players against Macclesfield - three through injury, while six were on international duty.
Pearson added: "That was the best side I could have fielded and it wasn't good enough. That's very frustrating.
"I'm not making excuses. We should have still had enough to beat Macclesfield. They've had two attempts I think and scored two goals."
Source: Team Talk
Source: Team Talk