This study evaluated the therapeutic efficacy of combining Neodymium-doped Yttrium Aluminum Garnet (Nd:YAG) laser with subgingival curettage and root planing (SRP) in generalised stage III/grade C periodontitis patients and its effects on cytokine dynamics and microbial community. Fifteen patients diagnosed with stage III/grade C periodontitis were included in the cohort. The right and left sides of the mouth were randomly assigned either the conventional SRP (control) group or the SRP supplemented with Nd:YAG laser group (experimental group, 160 mJ, 4 W) in a split-mouth design. Clinical periodontal indices were recorded at baseline and at the 6-week follow-up post-treatment. ELISA was utilised to measure IL-1β and TNF-α levels in gingival crevicular fluid. The subgingival microbiota's composition and variations were characterised using 16S rDNA amplicon sequencing, while quantitative real-time polymerase chain reaction (qRT-PCR) was employed to analyse the changes in the red-complex bacteria in subgingival plaque. The SRP+Nd group exhibited a statistically significant reduction in record probing depth (PD) and bleeding on probing (BOP) compared to the SRP group after treatment (p0.05). The SRP+Nd group showed a markedly lower IL-1β level than the SRP group (p0.05). Furthermore, there was no statistically significant difference in the dominant subgingival microbiota composition and level of the red-complex bacteria between the two groups (p>0.05). The adjunctive use of Nd:YAG laser with SRP demonstrates promising short-term therapeutic benefits for patients with extensive stage III/grade C periodontitis. Both SRP as a standalone treatment and its combination with Nd:YAG laser effectively facilitate a transition in the dominant bacterial community from periodontitis-associated to periodontal health-associated microbiota.