In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C-phycocyanin (C-PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C-PC were examined by model chemistry in gas phase at time-dependent density functional theory (TDDFT), configuration interaction-singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long-range pigment-protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short-range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long- and short-range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6-31+G* level were in good agreement with the experimental results of C-PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C-PC monomer is predominant from β-155 to β-84 (1/K = 13.4 ps), however, from α-84 of one monomer to β-84 (1/K = 0.3–0.4 ps) in a neighbor monomer in C-PC trimer. In C-PC hexamer, an additional energy flow was predicted to be from β-155 (or α-84) in top trimer to adjacent β-155 (or α-84) (1/K = 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc.