Objective To investigate the effect of zirconia all-ceramic inlay crown restoration of short crown molars after root canal therapy on periodontal health indexes. Methods A total of 72 patients with short crown molars admitted to the Department of Stomatology, Guanyun People's Hospital from January 2023 to February 2024 were selected as the research subjects. According to the different restoration methods, they were divided into control group and study group, with 36 patients in each group. Both groups were treated with root canal therapy before restoration, and the control group was given conventional metallo-ceramic crown, while the study group was given zirconia all-ceramic inlay crown. The restoration effect, periodontal health indexes and gingival crevicular fluid-related inflammation indexes were compared between the two groups. Result The proportion of gingival health, complete restoration, color matching and edge smoothness in the study group were all higher than those in the control group (P <0.05). AL, PLI, PD and BOP after restoration in the two groups were better than those before restoration, and those in the study group were better than those in the control group (P <0.05). IFN-γ, MMP-2, SOD and GP-x after restoration in the two groups were better than those before restoration, and those in the study group were better than those in the control group (P <0.05). Conclusion The application of zirconia all-ceramic inlay crown in the restoration of short crown molars can protect periodontal health, reduce the expression level of inflammatory factors in gingival crevicular fluid, and the restoration effect is good.