Abstract Background (−)-Epigallocatechin Gallate (EGCG) as green tea catechins possessed antibacterial and anti-inflammatory effects on periodontal disease. This study was designed to evaluate the clinical and microbiological efficacy of scaling and root planing (SRP) using EGCG aqueous solution as coolants through a new-type ultrasonic scaler tip on chronic periodontitis. Methods This split-mouth, randomized clinical trial included 20 patients (2 drop-outs) with chronic periodontitis and the maxillary contra-lateral sides were allocated into test and control groups randomly. Through the new-type scaler tip, 762 sites with probing depth (PD) ≥ 4 mm were treated by SRP using EGCG solution or distilled water as coolants respectively. Clinical parameters and red complex pathogens in subgingival microbiome were evaluated at baseline, 3 and 6 months after treatments. Results During 6 months, the SRP plus EGCG medication contributed to additional PD reduction as 0.33 mm and gain of clinical attachment level as 0.3 mm compared with SRP alone, and approximate 8% more sites obtained PD reduction ≥ 2 mm (p