Abstract Background Periodontitis is a chronic and multi-factorial infectious disease. A notable difference exists in the prognosis of patients with severe periodontitis after non-surgical periodontal treatment. Thus, a retrospective study was conducted to identify common and specific factors that impact the prognosis of patients with periodontitis stage III-IV following non-surgical periodontal treatment at different tooth sites. Methods A total of 977 teeth were included in the study, comprising 266 patients diagnosed with periodontitis stage III-IV. This sample included 330 anterior teeth, 362 maxillary posterior teeth, and 285 mandibular posterior teeth. Following treatment, the teeth were categorized into two groups based on residual pocket depth [probing depth (PD) ≥ 5 mm] at 3 months post-treatment. The prognosis of periodontitis stage III-IV was assessed through multivariate analysis employing logistic regression to determine the association of various risk factors. Results The PD values of each site and the deepest PD values of each tooth significantly decreased at 3 months post-treatment. Residual pockets were predominantly found in the mesio/disto-buccal and mesio/disto-lingual regions. Multivariate analysis revealed that gender, PD, sulcus bleeding index (SBI) and plaque index (PLI) at baseline, and crown-root ratio in anterior teeth had a significant influence on periodontitis stage III-IV (P