In this work, reclaimed water treated with sodium hypochlorite (NaClO) or chlorine dioxide (ClO2) at 1, 2, and 4 mg/L was operated successively for 30 days respectively, in annular reactors with new cast iron coupons, corresponding to stages I (days 0–30), II (days 31–60), and III (days 61–90). The Illumina HiSeq 2500 sequencing platform was used to analyze the bacterial community composition, scanning electron microscopy and X-ray diffraction analyses were conducted to characterize corrosion scales, and the weight loss method was served to determine the general corrosion rate. Results reveal the precise disinfection effect on biofilm bacteria to be dose dependent and species specific. In stage I, disinfection caused a reduction in the number of operational taxonomic units, but, had little effect on biofilm composition. In stage II, NaClO and ClO2 induced a reduction of Proteobacteria proportion, but increased the dominance of Firmicutes; the diminished Proteobacteria in NaClO test mainly included Gammaproteobacteria, while, that in ClO2 test mainly included the Gammaproteobacteria and Betaproteobacteria. In stage III, Firmicutes presented a certain resistance to NaClO and ClO2 as the accumulation of corrosion scales. Results also indicated that disinfection enhanced the corrosion process, and the promoting effect of ClO2 was more pronounced than that of NaClO. Moreover, this promoting effect was more obvious in stage I than that in the latter two stages. The strong oxidization effect associated with disinfection in stage I was the dominant factor promoting corrosion, whereas, the bacterial community also played a crucial role in stages II and III.