Mineral trioxide aggregate (MTA), the standard pulp capping material, has disadvantages, including long setting time and high cost. Along this line, acemannan, a polysaccharide extracted from aloe vera, would be a promising biomaterial for vital pulp therapy as it is shown to induce mineralized bridge formation in animal and clinical studies. In this study, the impact of MTA and acemannan sponges on partial pulpotomized permanent teeth has been evaluated. For the research design, fifty immature permanent teeth with caries or accident-induced pulp exposure were collected and assessed. After partial pulpotomy, the teeth were randomly allocated into the treatment group using either acemannan or the MTA group (n = 25). To conduct the study, the patients were examined immediately right after the treatment (baseline) and a follow-up period of 6- and 12-months post-surgery for clinical and Cone beam computed tomography (CBCT) examinations. We also designed and conducted the three-dimensional (3D) analysis to evaluate the apexogenesis impact of the two materials (MTA and acemannan) on the partial pulpotomy treatment, typically for the cases of immature permanent teeth. The evaluation results show that the overall success rate in the acemannan and MTA groups from baseline to 12-month follow-up was 90.91% and 95.65%, respectively, with no significant difference between the two groups when p > 0.05. In the success samples in both groups, the root length is increased and the apex size is decreased significantly (p < 0.05), indicating the continued root formation. The study then suggests that acemannan is a promising and beneficial alternative pulp capping material with low-cost for partial pulpotomy treatment for immature permanent teeth dedicated to vital pulp therapy in which we utilize the 3D-superimposition and apical foramen area as the novel reliable tools for the evaluations and analyses.