Employing the Mueller matrix method with polar decomposition, we analyse the polarization rotation (PR) effects in semiconductor optical amplifiers (SOAs) and demonstrate that the PR angle is linear to the birefringence dependent gain while the average PR coefficient is about 0.625 for the employed SOA. It is further evident that the current and optical intensity dependent PRs rotate reversely around the same axis. Thus we propose an optical-electric synchronous control scheme to obtain orthogonal polarization states with power-equalization, and implement it by a polarization-sensitive SOA. The polarization duration time is about 10 ns which is applicable to high-speed polarization state generation.