He said: "I hope it will recognise this and reconsider its view in advance of the public inquiry. If it is wrong and we lose our financial edge over other world cities such as Frankfurt and Berlin, London's economy will not recover in 100 years."
EH vetoed the 222 m tower in February, despite support from the Corporation of London and the Commission for Architecture and the Built Environment. The scheme now faces a DETR inquiry.
Livingstone added that he had held a fruitful meeting with EH in which it agreed that there should be a cluster of tall buildings to the north-east of the City, which could includes the former Bishopsgate goods yard near the Heron Tower site.
In a statement released at the conference, entitled Tall Storeys and held at the RIBA, EH defended its role. Chief executive Pam Alexander warned that the economic reasons for tall buildings were weak.
She added: "London has flourished as a world city because of its ability to strike a balance between continuity and change."