Based on the crystal structure and spectral properties of C-phycocyanin (C-PC) from cyanobacteria, models for complexes with 2 and 3 C-PC hexamer disks were built and the energy transfer dynamic properties were studied by the use of stochastic computer simulation approach. In addition, an experimental parameter of 0.056 ps-1, corresponding to a time constant of 18 ps, derived from the previous time-resolved measurement, was used for simulation of the energy transfer process from the three terminal symmetrically equivalent β84 chromophores of the core-linked disk to an α84 chromophore of the allophycocyanin (APC) core. The simulation showed: (1) The disk-to-disk energy transfer can be as fast as several picoseconds. (2) The energy transfer efficiencies from the first disk to the core would depend on the length of the rod (i.e. the number of disks). Efficiencies of 0.95, 0.87, and 0.75 were found for the rods with 1, 2 and 3 hexamer disks, respectively. (3) The energy transfer along a rod in a native phycobilisome (PBS) is probably very close to the one-way manner. It is the core of PBS that makes the excitation energy be transferred fast in a nearly one-way manner. and Jie Xie, Jing-quan Zhao, Chenghang Peng.