Two Sequencing Batch Reactors (SBR) systems, namely, the 'anaerobic-aerobic' alternative system denoted by System 1 and the 'anaerobic + aerobic' tandem system(denoted by System 2), applied to treating Reactive Turquoise Blue (RTB) contained synthetic wastewater were systematically investigated. The performance of each system in COD and RTB removals was traced throughout the experiment. The discrepancies of the two systems in RTB removal were compared and the reason for these discrepancies was explored. The results showed that both systems had high adaptability and sound stability, and could remove pollutants efficiently. As far as RTB removal, the anaerobic phase of System 1 was more efficient than that of System 2, and the aerobic phase of System 2 was more efficient than that of System I. The overall RTB removal rate of System 2 was higher than that of System I. These discrepancies between the two systems were explained by their different bio-face compositions, which was verified by examining the bio-faces.