Objective To explore the effect of root canal filled with warm vertical compaction and cold lateral condensation. Methods A total of 200 patients who underwent root canal treatment in our hospital from September 2019 to November 2022 were randomly divided into control group and observation group, with 100 patients in each group. The control group was treated with cold lateral condensation, and the observation group was treated with warm vertical compaction. The clinical efficacy, periodontal index and pain incidence were compared between the two groups. Results The total effective rate of treatment in the observation group was 97.00%, which was higher than 89.00% in the control group, and the difference was statistically significant (P <0.05). The periodontal index levels of the two groups immediately after treatment and 3 months after treatment were lower than those before treatment, and those in the observation group were lower than those in the control group, the difference was statistically significant (P <0.05). The incidence of pain in the observation group was 21.00%, which was lower than 37.00% in the control group, and the difference was statistically significant (P <0.05). Conclusion The application of warm vertical compaction in root canal therapy can effectively improve the periodontal index of patients and reduce the incidence of pain, which is better than the cold lateral conden sation.