The confirmation and allocation of initial carbon dioxide emissions are the preconditions of carbon emissions trading market. Based on the harmony theory,three pairs of equilibriums namely supplydemand equilibrium, regionalindustry equilibrium and equityefficiency equilibrium are considered. The connotation and thinking of harmonious allocation for initial carbon dioxide emissions are analyzed. The harmonious allocation methods and theoretical frame of initial carbon dioxide are put forward. Firstly,Based on carbon emissions control target, scenario analysis theory and interval mathematics theory, the preallocation model of initial carbon dioxide emissions is set up to get preconfigured plan. Secondly, to evaluate the harmonious degree of the preconfigured plan, the harmonious evaluation model is established. Thirdly, on the basis of improving preconfigured plan failed to pass the harmonious evaluation, the harmonious evolution model is obtained.