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Biodesulfurization under haloalkaline conditions requires limiting oxygen and additional energy in the system to deliver high mixing quality control. This study considers biodesulfurization in an airlift bioreactor with uniform microbubbles generated by a fluidic oscillation aeration system to enhance the biological desulfurization process and its hydrodynamics. Fluidic oscillation aeration in an airlift bioreactor requires minimal energy input for microbubble generation. This aeration system produced 81.87% smaller average microbubble size than the direct aeration system in a bubble column bioreactor. The biodesulfurization phase achieved a yield of 94.94% biological sulfur, 84.91% biological sulfur selectivity, and 5.06% sulfur oxidation performance in the airlift bioreactor with the microbubble strategy. The biodesulfurization conditions of thiosulfate via Thioalkalivibrio versutus D306 are revealed in this study. The biodesulfurization conditions in the airlift bioreactor with the fluidic oscillation aeration system resulted in the complete conversion of thiosulfate with 27.64% less sulfate production and 10.34% more biological sulfur production than in the bubble column bioreactor. Therefore, pleasant hydrodynamics via an airlift bioreactor mechanism with microbubbles is favored for biodesulfurization under haloalkaline conditions.