Objective To investigate the effect of different root canal fillers in the treatment for endodontic diseases.Methods A random number table method was used to select patients with endodontic disease admitted to the Third People's Hospital of Nanyang City from January 2020 to February 2023, and 64 cases were selected as research objects during the screening period. All patients were treated with root canal filling. According to the different root canal filling materials used, the patients were divided into 3 groups. Group A (20 cases) was filled with zinc oxide clove oil paste, group B (22 cases) was filled with nano-hydroxyapatite, and group C (22 cases) was filled with AH-plus paste. The clinical effects, teeth bite force, bleeding index, gingival index and the incidence of adverse reactions among the three groups were compared.Results The total clinical effective rate of group A was 65.00%, group B was 81.81%, and group C was 90.91%, which was lower in group A than in group B and group C (P<0.05). After treatment, the level of tooth biting force in group B and group C was higher than that in group A (P<0.05); the bleeding index and gingival index of group B and group C were lower than those of group A (P<0.05). The incidence of adverse reactions in group A was 30.00%, group B was 13.64%, and group C was 4.55%. The incidence of adverse reactions in group B and group C was lower than that in group A (P<0.05).Conclusion AH-plus paste has the best clinical effect, and the therapeutic effect of nano-hydroxyapatite is second only to AH-plus paste, which can enhance the teeth biting force, reduce the bleeding index and gingival index, alleviate the occurrence of adverse reactions after treatment, and effectively improve the oral environment.