Objective To investigate the effect of polymeric ceramic onlay restoration on periodontal index in patients with short crown molars after root canal therapy. Methods From January 2020 to June 2021, 60 patients with short crown molars admitted to the Department of Stomatology, Guizhou Provincial People's Hospital were selected as the research subjects. According to the different treatment methods, they were divided into control group and observation group, with 30 patients in each group. The control group was restored with polymeric all-ceramic crown, and the observation group was restored with polymeric ceramic onlay. The periodontal index, restoration effect, oral function and inflammatory factor level were compared between the two groups. Results After treatment, the BI, PLI, and PD in the observation group were lower than those in the control group (P <0.05). The total effective rate of restoration in the observation group was 96.67%, which was higher than 90.00% in the control group, but the difference was not statistically significant (P >0.05). After treatment, the scores of language function, retention function and mastication function in the observation group were higher than those in the control group (P <0.05). After treatment, the levels of CRP and TNF-α in the observation group were lower than those in the control group (P <0.05). Conclusion The effect of polymeric ceramic onlay for restoration of short crown molars after root canal therapy is good, which can improve patients’ periodontal index, promote the recovery of oral function, and is beneficial to reducing the level of inflammatory factor and improving the quality of life, which is worthy of clinical application.