Background: Facial soft tissue thickness (FSTT) is a fundamental parameter in forensic facial reconstruction; however, direct comparative data across major Asian subpopulation groups remain limited. To date, no study has directly compared the FSTT characteristics of Southeast Asian and East Asian populations. This study addresses this gap by comparing Indonesian (Southeast Asian) and Japanese (East Asian) populations across 36 facial landmarks. Methods: FSTT measurements were obtained from Indonesian (n = 206) and Japanese (n = 251) adults. A supine correction factor was applied to all supine-acquired datasets to standardize measurements to upright equivalence before analysis. Analysis of Covariance (ANCOVA) was performed to compare FSTT between populations while adjusting for age, sex, body mass index (BMI), and modality. Bonferroni correction was applied to account for multiple comparisons. Additional stratified analyses were conducted to evaluate the consistency of observed differences across demographic subgroups. Results: After adjustment for age, sex, and BMI, ANCOVA identified significant population differences in 12 of 36 landmarks following Bonferroni correction (p < 0.0014; partial η² ≈ 0.06–0.13). Indonesians showed greater thickness at anterior midline landmarks (Pr, Id), whereas Japanese individuals exhibited higher values in midfacial (Al, Zm), temporomandibular (Kdl), and mandibular (Spm2, Sm2) regions. Stratified analyses confirmed consistent patternsacross age, sex, and BMI, with age-related thinning, greater FSTT in males, and strong positive associations with BMI. Conclusion: While overall FSTT patterns are broadly similar, several population-specific differences persist after covariate adjustment, highlighting the importance of considering intra-Asian population context in forensic facial reconstruction. © 2026 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license. http://creativecommons.org/licenses/by-nc-nd/4.0/