Two conjugates of R-phycoerythrin (R-PE) and C-phycocyanin (C-PC) were synthesized through a coupling agent, N-succinmidyl 3-(2-pyridyldithio)-propionate and the alternation of the ratio of R-PE to C-PC. Their ratio of R-PE to C-PC were determined by absorption spectra. One is 6∶1, the other is 2∶1. The phenomena of intramolecular energy transfer were characterized. The calculated results showed that the efficiency of energy transfer from R-PE to C-PC was 63% and 88% respectively. The efficiency of energy transfer is better. When the disulfide bridge between R-PE and C-PC was reduced by DTT, the energy transfer was stopped. The phenomena further verified the intramolecular energy transfer from R-PE to C-PC.