BackgroundLarge to giant congenital melanocytic nevi (LGCMN) significantly decrease patients' quality of life, but the inaccuracy of current classification system makes their clinical management challenging.ObjectivesTo improve and extend the existing LGCMN 6B/7B classification systems by developing a novel LGCMN classification system based on a new phenotypic approach to clinical tool development.MethodsThree hundred and sixty‐one LGCMN cases were categorized into four subtypes based on anatomic site: bonce (25.48%), extremity (17.73%), shawl (19.67%) and trunks (37.12%) LGCMN. A ‘BEST’ classification system of LGCMN was established and validated by a support vector machine classifier combined with the 7B system.ResultsThe most common LGCMN distributions were on bonce and trunks (bathing trunk), whereas breast/belly and body LGCMN were exceptionally rare. Sexual dimorphism characterized distribution, with females showing a wider range of lesions in the genital area. Nearly half of the patients with bathing trunk LGCMN exhibited a butterfly‐like distribution. Approximately half of the LGCMN with chest involvement did not have nipple–areola complex involvement. Abdomen, back and buttock involvement was associated with the presence of satellite nevi (r = 0.558), and back and buttock involvement was associated with the presence of nodules (r = 0.364).ConclusionsThe effective quantification of a standardized anatomical site provides data support for the accuracy of the 6B/7B classification systems. The simplified BEST classification system can help establish a LGCMN clinical database for exploration of LGCMN aetiology, disease management and prognosis prediction.