BISURE (BIological SUlfide REmoval) systems are efficient biological systems for sulfide removal and elemental sulfur recovery. However, they often suffer from disturbance caused by filamentous sludge bulking during startup, which are inoculated with activated sludge. In this study, BISURE startup by increasing the influent substrate concentration (IC-mode) and speeding up the influent flow rate (IF-mode) were investigated to understand and avoid the disturbance. The results showed that the BISURE system could be successfully started up in both the IC mode and IF mode, but both modes could trigger filamentous sludge bulking by Thiothrix (a filamentous sulfur-oxidizing bacteria, F-SOB). “CSO going first, PSO following up” was an effective approach to control the filamentous sludge bulking during startup. The procedure mechanism of oxygen effect was revealed: the growth of zoogloeal SOB (Z-SOB) with its larger surface-to-volume ratio (SVR) was first promoted to achieve a “proportion advantage” over F-SOB in the bacterial community; the external location of Z-SOB was then fixed to achieve the “location advantage” over F-SOB in the sludge floc; finally, prior uptake of DO by Z-SOB was ensured to achieve a “sequence advantage” over F-SOB in the substrate utilization. After elimination of filamentous sludge bulking, the dominant SOB in the bacterial community in IC-mode were Thiobacillus, accounting for more than 90% of the population; while dominant SOB in IF-mode were Thiobacillus and Annwoodia, which together accounted for more than 60% of bacteria. These findings are helpful in characterizing biological desulfurization and going forward, should be important in further developing BISURE systems.