This study establishes standardized necropsy protocols and describes the anatomical characteristics of greater horseshoe bats (Rhinolophusferrumequinum), with sex-based comparisons and interspecific analysis. Six deceased bats (4 males, 2 females) were collected from South Korea between May and August 2025. Comprehensive necropsies were performed following Biosafety Level 2 protocols. Body weight showed no significant sexual dimorphism (females: 18.23 ± 1.26 g; males: 17.22 ± 3.42 g; p = 0.720). Of 13 morphometric parameters, only the second digit length (D2) was significantly longer in males (40.00 ± 0.82 mm) than females (36.50 ± 2.12 mm; p = 0.034). Internal anatomy revealed flight adaptations, including pectoral muscles comprising >80% of muscle mass, asymmetric two-lobed lungs, and a 170 mm intestinal tract where the stomach and cecum were indistinct. Males exhibited symmetrical, white, round testes (5 mm diameter) located 15 mm from the abdominal cavity. Mild hepatic lipidosis was observed in 33% of specimens, but no parasites or wing lesions were found. Comparative analysis with Miniopterusfuliginosus from Jeju Island highlighted interspecific differences in body size and morphology. This study provides essential baseline data for the health monitoring and conservation management of Korean bat populations.