Diana Holland said Labour's relationship with the unions delivered financial stability for the party and helped ensure it had cut its debt from £27 million to £2 million in eight years.
The party should be debt- free by June 2016, Ms Holland said, but warned its "proven" financial model could be harmed if the Labour leadership changes its relationship with the unions.
Mr Miliband wants union members to opt into party membership rather than be automatically affiliated, a controversial move which led the GMB to decide to cut its affiliation funds to Labour by over £1 million from next year.
A special conference is planned for March when the changes are expected to be adopted following a report by the Labour peer Lord Collins.
Ms Holland warned against any changes which would hit the party's finances.
She said: "Looking ahead we have a number of financial hurdles to clear.
"Next year, we have the European elections campaign and Scottish referendum, local elections and of course the general election in 2015."