Objective To compare the long-term effects of zirconia all-ceramic crown (ZAC) and porcelain-fused-to-metal crown (PFM) in restoring posterior tooth defect. Methods A total of 102 patients with posterior tooth defect admitted to the Department of Stomatology, Langao County Hospital from January 2020 to May 2022 were selected as the research subjects, and they were divided into the control group and the observation group according to the random number table method, with 51 patients in each group. The control group was restored with PFM, and the observation group was restored with ZAC. The patients were followed up for 3 years after restoration, and the restoration effect and periodontal indexes were compared between the two groups immediately after surgery and at 1 and 3 years after surgery. Results There were no significant differences in the qualified rate of restoration integrity and marginal adaptation between the two groups immediately after surgery and at 1 year after surgery (P >0.05). The qualified rate of restoration integrity and marginal adaptation in the observation group at 3 years after surgery was higher than that in the control group (P <0.05). There was no significant difference in the qualified rate of gingival reaction between the two groups immediately after surgery (P >0.05). The qualified rate of gingival reaction in the observation group at 1 and 3 years after surgery was higher than that in the control group (P <0.05). There were no significant differences in the incidence of secondary caries between the two groups at different periods (P >0.05). There were no significant differences in PLI and GI between the two groups immediately after surgery (P >0.05). The PLI and GI in the observation group at 1 and 3 years after surgery were lower than those in the control group (P <0.05). Conclusion Compared with PFM, ZAC has more ideal long-term effects in restoring posterior tooth defect, with better performance in restoration integrity, gingival reaction and maintenance of oral hygiene.