Objective To detect the composition of the subgingival microbiota in generalized aggressive periodontitis (GAgP) and severe chronic periodontitis (SCP) patients tested by high-throughput sequencing (HTS) technologies, analyze its diversity and function by using bioinformatics, and observe changes in the subgingival microbiota before and after periodontal initial therapy. Methods Eleven patients with GAgP and 14 patients with SCP who visited the Department of Periodontics in Stomatological Hospital of Kunming Medical University from September 2018 to May 2019 were recruited, and subgingival plaque samples were collected at baseline and 6 weeks after initial therapy. Then, the genomic DNA was distracted and sequenced by the Illumina MiSeq high-throughput sequencing platform. QIIME (quantitative insights in microbial ecology), Mothur, SPSS and other software were used to analyze community information. LEfSe difference analysis (linear discriminant analysis effect size), network analysis, and the KEGG PATHWAY database (https://www.kegg.jp/kegg/pathway.html) were used to predict community function. Results At baseline, the dominant microbiota of GAgP and SCP patients were similar, including Bacteroidetes, Porphyromonas and Porphyromonas endodontalis. Six weeks after initial therapy, as the periodontal pocket became shallower, the variation trend of the microbiota of GAgP and SCP patients was similar. The relative abundance of gram-negative bacteria, such as Bacteroidetes, Porphyromonas and Porphyromonas endodontalis, decreased, while the relative abundance of gram-positive bacteria, such as Proteobacteria, Actinomyces and Rothia aeria, increased. Actinobacteria were significantly increased biomarkers of the subgingival microbiota in GAgP after treatment. Streptococcus is an important genus that connects the microbiota related to periodontitis and the microbiota related to periodontal health. Community function prediction result showed that initial treatment can reduce the functions of amino acid metabolism, methane metabolism, and peptidase in GAgP and SCP patients. Conclusion The subgingival microbiota of GAgP and SCP patients are similar. Streptococcus, as an early colonizer, may play an important role in promoting plaque biofilm formation and maturation in the process of subgingival flora from health to imbalance. Initial therapy can change the composition and structure of the subgingival microbiota, reduce community diversity, and reduce the functions of amino acid metabolism, methane metabolism, and peptidase in GAgP and SCP patients.