It is urgently necessary to clarify the effect of extraction of impacted mandibular third molar (IMTM) on the periodontal tissue of adjacent second molars (ASMs). In this study, the ASM periodontal condition and pathogenic microbes were assessed before IMTM extraction and at 1, 4, 8 and 12 weeks postoperatively. Based on the inclusion and exclusion criteria, our study revealed that IMTM extractions adversely affected distal - periodontal probing depth (dPPD), attachment loss (dAL), plaque index (dPLI) and bleeding on probing (dBOP) within 8 weeks, but these indices gradually normalize after 12 weeks. The subgingival pathogens near the ASMs distal surface, Porphyromonas and Pseudomonas, were significantly increased postoperatively. Moreover, relevance of ASMs clinical indices and subgingival microbes after IMTM extractions was found. In contrast to the situation in chronic periodontitis, the effects of IMTM extraction on dPPD, dAL, dPLI and dBOP of ASMs were mainly correlated with Pseudomonas. Additionally, while the IMTM extractions have adverse distal periodontal indices of ASMs within 8 weeks and increase subgingival pathogens, the modified triangular flap (MTF) had fewer distal periodontal indices and less Pseudomonas. Compared to the traditional envelope flap and triangular flap, the MTF benefits the periodontal health, which could be considered as the priority option for IMTM extractions.