Background/Objectives: To evaluate whether automated three-dimensional (3D) volumetric body composition metrics derived from the Body and Organ Analysis (BOA) algorithm provide prognostic information beyond body mass index (BMI) for overall survival (OS) in patients with surgically treated head and neck squamous cell carcinoma (HNSCC), and to compare cervical (C1–C7) measurements with thoracic and abdominal benchmarks. Methods: This single-center retrospective cohort study included 391 surgically treated HNSCC patients at Universitätsmedizin Greifswald (2010–2019). Patients with definitive (chemo)radiation (no surgery) or non-standard adjuvant chemotherapy alone (n=13) were excluded; thus, all included patients had primary surgical management. Tumor staging was retrieved from institutional records for all 391 patients. For patients with documented ongoing follow-up but without a specific last-contact date, survival status was verified by chart review where possible, and patients confirmed alive at the institutional database snapshot date were administratively censored on 28 January 2025. Pretreatment CT scans were processed using the open-source BOA algorithm (v0.1.3) to obtain volumetric tissue measurements of muscle, bone, and adipose compartments across abdominal, thoracic, and cervical (C1–C7) regions. Composite indices — Sarcopenia Index (SI = Muscle/Bone) and Myosteatotic Fat Index (MFI = IMAT/TAT) — were derived. Univariate and multivariate Cox proportional hazards models were used. The primary clinically adjusted model included cervical SI, age, sex, tumor site, UICC stage, treatment modality, the Head and Neck Charlson Comorbidity Index (HN-CCI), and secondary malignancy; a minimally adjusted model (HN-CCI and secondary malignancy) was retained as a supportive analysis. Leukocytes and postoperative CRP were examined in a sensitivity model. Reporting followed the STROBE checklist. Results: Of 391 evaluable cases (91% male, median follow-up 5.0 years, 141 deaths), BMI showed only a weak univariate association with overall survival (HR 0.84, p=0.052) and was not independently associated with OS after adjustment (multivariate HR 0.88, p=0.15). In contrast, in the minimally adjusted supportive model the cervical Sarcopenia Index (Cerv SI, Muscle/Bone) was associated with overall survival (HR 0.71, 95% CI 0.58–0.88, p=0.002); in the primary clinically adjusted model including age, sex, tumor site, UICC stage, treatment modality, HN-CCI, and secondary malignancy, cervical SI remained independently associated with OS (HR 0.75, 95% CI 0.61–0.92, p=0.007; n=254). Thoracic Myosteatotic Fat Index (Thor MFI) was associated with worse overall survival in the minimally adjusted supportive model (HR 1.35, p=0.002) and remained associated after extended oncologic adjustment (HR 1.26, p=0.013). Harrell's concordance index for overall survival prediction was 0.60 for cervical SI and 0.55 for BMI; the difference was modest. Inter-regional SI correlations were strong between abdomen and thorax (r=0.69) but only moderate for cervical–thoracic (r=0.42). An in-sample comparison showed that a BOA-derived single-level C3 Sarcopenia Index was non-prognostic (C-index 0.52) and weakly correlated with the volumetric C1–C7 SI (r=0.04), suggesting that the volumetric and single-vertebra-level metrics derived from the BOA pipeline capture different information. In paired bootstrap comparisons, cervical SI showed a modest but significant C-index improvement over BMI (ΔC = +0.087, p = 0.038) but did not significantly outperform the BOA-derived C3 SI, ASA classification, or thoracic SI. Conclusions: BOA-derived volumetric body composition indices, particularly the cervical Sarcopenia Index, are associated with overall survival in surgically treated HNSCC patients and remain prognostic after adjustment for established oncologic confounders, whereas BMI is not. Cervical C1–C7 BOA analysis enables body composition assessment from routine head and neck CT and may provide an objective imaging-derived marker for future risk-stratification studies. Prospective validation and formal comparison with established C3/L3 methods are warranted before routine clinical use.