Background: Competency-based medical education has emerged as a mainstream method for educating and assessing the next generation of physicians. This study aims to initiate and examine the preliminary results of an integrated Traditional Chinese Otolaryngology Milestone Project in Taiwan. Methods: This prospective study enrolled 18 participants in an academic hospital setting from July 2017 to August 2019. Participants included twelve attending and six resident physicians. Using the Integrated Traditional Chinese Otolaryngology Milestones (ITCOM), five biannual evaluations involved independent self-assessments by the resident doctors, which the chief resident and attending physicians independently reevaluated. A Kruskal–Wallis test was used to compare the results of the five assessments. Results: The average scores of attained milestones for the five assessments were as follows for residents PGY1– PGY6: PGY1 (1.48 ± 0.24; 1.69 ± 0.10, P = 0.01), PGY2 ( 1.24 ± 0.12; 1.51 ± 0.23; 1.75 ± 0.06; 1.98 ± 0.21; 2.47 ± 0.18 , P < 0.0001), PGY3 (2.19 ± 0.24; 2.36 ± 0.25; 2.80 ± 0.19; 2.96 ± 0.24; 3.33 ± 0.23, P < 0.0001), PGY4 (2.68 ± 0.17; 2.96 ± 0.09; 3.35 ± 0.13; 3.58 ± 0.10; 4.17 ± 0.08, P < 0.0001), PGY5 (3.07 ± 0.24; 3.38 ± 0.12; 3.58 ± 0.10; 4.05 ± 0.09, P < 0.0001) and PGY6 ( 3.30 ± 0.27; 3.61 ± 0.28; 4.22 ± 0.20, P = 0.0001). The score results for patient care, medical knowledge, and professionalism were more likely to indicate heightened attainment of milestone levels as the program progressed. However, the curves of the score results for system-based practice, problem-based learning and improvement, and interpersonal and communication skills were more horizontal, showing that the milestones might indicate a better performance than expected, even in residents with low training seniority. Conclusions: The results of the five biannual assessments revealed that all resident physicians demonstrated a significant improvement. Further study involving large-scale participants and multiple institutions is warranted.