Background: We have modified the internal sinus elevation by combining it with the sinus mucoperiosteum stripping procedure, which further increases the indications for the internal lift. Similar long-term clinical follow-up studies and three-dimensional finite element analyses are rare.Objective: This study aimed to investigate the feasibility of the modified internal sinus floor elevation method in patients with low residual bone height using a three-dimensional (3D) finite element model and report on the long-term outcomes.Materials and Methods: Overall, 99 implants were placed in 86 patients. All patients were followed-up for 3-24 months. The modified internal sinus floor elevation was dynamically simulated using a 3D finite element model, and the stress of the sinus membrane was measured.Results: In trial group A (modified internal sinus floor elevation group), 57 implants were placed in 52 patients. The sinus floor height was lifted by 6.5 mm (95%confidence interval (CI): 6.2-6.8). The perforation rate was 8.8%, and the implant survival rate was 96.5%. In control group B (external sinus floor elevation group), 42 implants were placed in 34 patients. The sinus floor height was lifted by 8.8 mm (95%CI: 8.4-9.3). The perforation rate was 14.3%, and the implant survival rate was 100%. In trial group A, compared with the control group B, perforation decreased by 5.5% (odds ratio = 0.50 and 95%CI: 0.14-1.78; p = 0.282), and the sinus floor lift height was 2.3 mm lower (95%CI, 1.8-2.9; p < 0.001). The finite element analysis showed that the peak stress of the sinus membrane increased with an increase in height elevation and degree of membrane separation. Conclusion:Our findings indicate the positive clinical outcomes in patients with low RBH associated with the modified internal sinus elevation procedure.