Thieves stole a 5m (16ft 4in) flagpole - complete with Union Jack - at some point over the weekend.
Earlier this month, items intended for an open day, including two generators, food and drink were stolen.
Last year, a memorial to the thousands of crewmen who served in Bomber Command during World War Two was damaged by trespassers.
Director of the centre Nicky Barr said it was "extremely frustrating".
She said: "I had great faith in the human race, but it has been somewhat diminished -  I don't understand why someone would want to target a memorial."
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The Lincoln attraction is to honour the air crews' efforts with exhibitions, information and accounts from service personnel and survivors.
The centre - set to open in September - still needs Â£2m in donations and events are being held to raise the cash.
125,000
Aircrew served in Bomber Command in World War Two
364,514 operational sorties flown
55,573 aircrew killed in action
25,611 killed flying from Lincolnshire
70% of aircrew were killed, taken prisoner or injured
Mrs Barr said fundraising efforts were being hampered by the break-ins.
She said: "Whether it was done as high jinks, or whether there is a market for second-hand flag poles, I just don't know.
"The reality is the sacrifices made by these guys [Bomber Command crews] allows for the freedom whoever is doing this has got today."
Officials have launched a petition in a bid to get further funding from the government to complete the project.
The International Bomber Command Centre has been targeted by thieves for the second time in a matter of weeks.