The fruit mulberry industry is an important component of the diversified utilization of mulberry trees, and mulberry sclerotinia disease is one of the key factors restricting the development of this industry. Among these, hypertrophic sclerotinia disease, a common disease caused by Ciboria shiraiana, is widespread in major fruit-mulberry planting regions and poses a serious threat to the healthy development of the fruit-mulberry industry. Therefore, this study systematically evaluated the resistance of mulberry germplasm resources to hypertrophic sclerotinia disease using Ciboria shiraiana as the inoculation pathogen. A total of 421 mulberry germplasms were collected from the National Mulberry Germplasm Repository (Zhenjiang) for indoor detached leaf identification, among which 284 high-yielding germplasms were further subjected to field identification. A five-level resistance evaluation standard was established using the relative resistance index (RI) combined with K-means cluster analysis. The effects of germplasm type, species, and geographical origin on resistance were analyzed, and the correlation between resistance and main fruit nutritional components was also investigated. The results showed extremely significant differences in resistance among the tested germplasms, with a coefficient of variation of 121.54 % for field diseased fruit rate and an indoor disease development rate ranging from 0.17 to 4.16 cm2/ d. The average disease development rate of wild germplasms (1.07 ± 0.81 cm2/d) was significantly lower than that of cultivated germplasms (1.69 ± 0.75 cm2/d) (p < 0.001), demonstrating stable and superior resistance. Among different mulberry species, Morus cathayana exhibited the strongest resistance, while Morus alba and Morus multicaulis were generally susceptible. Geographical origin had no significant effect on resistance (p = 0.421), indicating that resistance is primarily determined by genetic background. Ten high-yielding and highly resistant varieties, including ‘Zhongshen 3’ and ‘72C002’, were selected (diseased fruit rate < 2.58 %, disease development rate < 0.99 cm2/ d). No significant correlations were found between disease resistance and quality traits such as total flavonoids and anthocyanins; however, a weak negative correlation was observed between disease development rate and total soluble sugar content in susceptible germplasms (p< 0.05). This study established an RI-based resistance evaluation system for mulberry germplasm, clarified the resistance differences among germplasms, and identified elite resistant sources, providing important references for disease-resistant breeding, rational germplasm deployment, and further research on resistance mechanisms.