To compare the clinical efficacy of bioceramic materials iRoot BP Plus and MTA in offending teeth of jaw cyst. Methods A total of 90 patients with jaw cysts admitted to the Department of Stomatology, Shanghai Jiading District Central Hospital from December 2019 to December 2021 were selected as the research objects. They were divided into iRoot BP Plus observation group, MTA observation group and control group by random number table method, with 30 patients in each group. The iRoot BP Plus observation group was filled with iRoot BP Plus to fill the lower 1/3 of the root canal, the MTA observation group was filled with MTA to fill the lower 1/3 of the root canal, and the control group was filled with traditional cold lateral condensation method. The immediate root filling of the affected teeth and the long-term clinical efficacy of the jaw cyst after 1 year were compared among the three groups, and the filling operation time of the lower 1/3 segment of the root canal was compared between the two observation groups. Results The root canal filling rate of the three groups was 100.00%, and the difference was not statistically significant (P >0.05). The operation time of 1/3 root canal filling in iRoot BP Plus observation group was shorter than that in MTA observation group (P <0.05). After 1 year of follow-up, the total effective rate of treatment in the iRoot BP Plus observation group was higher than that in the MTA observation group, but the difference was not statistically significant (P >0.05). The total effective rate of treatment in the two observation groups was higher than that in the control group (P <0.05). Conclusion The clinical effect of iRoot BP Plus and MTA in the treatment of root canal of offending teeth before jaw cyst surgery is better than that of traditional cold gutta-percha lateral pressure filling method. The clinical effect of iRoot BP Plus is similar to that of MTA,but iRoot BP Plus has short clinical operation time and is simple and convenient, ready to use, and is worthy of clinical application.