Mr Bell made the allegation while speaking under parliamentary privilege.
The advisers named by Mr Bell, Timothy Johnston and John Robinson, have denied the claims.
The DUP said the claims were "outrageous".
MLAs were debating the RHI scheme at Stormont.
A motion to delay the debate by a week, in the wake of the Secretary of State James Brokenshire's announcement of an election, was interrupted when Mr Bell made dramatic claims about the DUP.
Mr Bell said when he was enterprise minister his special advisor, Timothy Cairns, told him "he will not be allowed to reduce the tariff on (the RHI) scheme" because of Mr Johnston and Mr Robinson's "extensive interests in the poultry industry".
He added that he has "kept the records in many, many formats" and that he had been suspended from the party for "telling the truth".
He also claimed that Mr Robinson and Dr Andrew Crawford, a DUP party adviser, had issued instructions to "try not to get Arlene called to the Public Accounts Committee (PAC)" and "under no circumstance allow Jonathan Bell to be called" over their roles in the RHI scheme.
The DUP said the claims were "outrageous, untrue and unfounded" and "nothing short of mud-slinging".
They said that neither Mr Johnston nor Mr Robinson have interests in the poultry industry, and added that Mr Robinson's "family home farm have chicken houses but are not part of the RHI scheme and never have been recipients or applicants".
Mr Johnston, the special adviser to Arlene Foster when she was first minister, said: "I have no family connections to the poultry industry and I have no connection to the RHI scheme.
"These are unsubstantiated allegations. I have two brothers-in-law in the poultry industry. They have no connection to RHI."
Mr Robinson, special adviser to Economy Minister Simon Hamilton, said: "I have no personal interest in the poultry industry. Two of my brothers are poultry farmers but they have no connections to RHI."
Dr Crawford, a former special adviser to the Department of Finance, told the BBC last month that his brother is the director of a company which successfully applied to the RHI scheme.
He said: "I never sought to keep the RHI scheme open at the original higher tariff against the wishes of the minister."
Mr Bell broke ranks with his party and made serious allegations against the DUP over the scheme's operation in a BBC interview in December.
He claimed that DUP advisers had attempted to remove Mrs Foster's name from documents linked to RHI.
Mr Bell was later suspended from the DUP.
The RHI scheme was set up by former first minister Arlene Foster in 2012 when she was enterprise minister.
Its aim was to increase consumption of heat from renewable sources.
However, businesses received more in subsidies than they paid for fuel, and the scheme became heavily oversubscribed.
It could lead to an overspend of Â£490m over the next 20 years.
MLA Jonathan Bell has claimed he was told he would not be able to challenge the Renewable Heat Incentive (RHI) scheme because two DUP special advisers "have extensive interests in the poultry industry".