Purpose: The effectiveness of using different laser therapy strategies in adjunct to scaling and root planing (SRP) for treatment of periodontitis remains unclear. This study compared the treatment outcome of SRP and its combination with Er:YAG laser and/or photobiomodulation on patients with severe periodontitis. Materials and Methods: A total of 50 patients were included, whose teeth were divided into 4 quadrants: 1. SRP+Er:YAG laser irradiation+photobiomodulation treatment; 2. SRP+Er:YAG laser irradiation treatment; 3. SRP+photobiomodulation treatment; 4. SRP treatment only. An Er:YAG laser at powers of 50 or 40 mJ and an Nd:YAG laser at 50 mJ were used. Patients were followed-up for 3 months. Periodontal clinical parameters (probing depth [PD], clinical attachment level [CAL], plaque index [PLI] and bleeding index [BI]), inflammation factors (melatonin and MMP-8 levels) and pain intensity were compared among the 4 quadrants. Results: The quadrant treated by SRP combined with Er:YAG laser irradiation and photobiomodulation had statistically significantly lower PD (p = 0.0081 at 1 month; p < 0.0001 at 3 months), CAL (p = 0.003), PLI (p = 0.0011) and BI levels (p = 0.005 at 1 month; p = 0.0236 at 3 months) compared with the other 3 quadrants. In addition, melatonin (p = 0.0006 at 1 month; p = 0.0002 at 3 months) and MMP-8 levels (p = 0.0012; only at 1 month) were also statistically significantly higher. Conclusion: Of the treatments tested here, SRP combined with Er:YAG laser irradiation and photobiomodulation had the best short-term outcome for severe periodontitis.