Background: The optimal extent of cervical excision according to transformation zone anatomy remains uncertain. This study evaluated the association of transformation zone (TZ) type with surgical margin status, margin localization, and conization specimen dimensions and explored TZ-specific cone length estimates associated with negative surgical margins. Methods: This retrospective cohort study included 323 women who underwent cervical conization for high-grade squamous intraepithelial lesions (HSIL; cervical intraepithelial neoplasia grades 2 and 3 [CIN2–3]) between January 2022 and November 2025. TZ types were classified as TZ1, TZ2, or TZ3. Cone dimensions and surgical margin outcomes were compared across TZ types. Multivariable logistic regression was performed to evaluate factors associated with positive surgical margins, and receiver operating characteristic (ROC) analysis was used to explore overall and TZ-specific cone length estimates associated with negative surgical margins. Results: Overall positive surgical margin rates did not differ significantly across TZ types (TZ1, 18.2%; TZ2, 12.0%; TZ3, 19.0%; p = 0.319). In the multivariable model excluding surgical excision dimensions, TZ type was not significantly associated with margin positivity. In a separate conditional-on-length model, TZ2 (OR 3.94, 95% CI 1.36–11.43) and TZ3 (OR 6.92, 95% CI 2.40–20.00) were associated with higher odds of positive margins compared with TZ1, whereas greater cone length was associated with lower odds of margin positivity (OR 0.037, 95% CI 0.014–0.099). Conclusions: TZ type was associated with distinct patterns of surgical margin localization following cervical conization. Although overall margin positivity did not differ significantly across TZ types, the conditional-on-length analysis indicated that the relationship between TZ anatomy, excision length, and margin status is interdependent. These findings highlight the relevance of TZ anatomy when interpreting surgical margin patterns, while the proposed TZ-specific cone length estimates remain exploratory and require prospective external validation before clinical application.