Rice bakanae disease, caused by the seed-borne fungus Fusarium fujikuroi, is a fungal disease primarily characterized by symptoms such as excessive elongation of seedlings, which can lead to plant death in severe cases. Currently, chemical control remains the primary method for managing this disease. The evaluation of bakanae disease standards for resistance in rice germplasm resources remains diverse and lacks unifies standards. The seedling stage is a critical period determining the occurrence of bakanae disease. To address this, a comprehensive resistance index was developed based on the elongation rate and seedling death rate at the seedling stage, using 99 rice germplasm resources (including 45 early indica rice, 30 late japonica rice, and 24 three-line sterile lines) to evaluate their resistance. The results revealed that only two out of the 99 germplasms exhibited resistance. Among them, the early indica rice line ‘Zhongfanzao E67’ had a comprehensive index of 1.8, rated as “resistant”, while the late japonica rice variety ‘Zhegeng 98’ had an index of 3.8, rated as “moderately resistant”. Among the remaining 97 susceptible materials, moderately susceptible, susceptible, and highly susceptible germplasms accounted for 22.22%, 16.16%, and 59.60% of the total, respectively. Additionally, japonica rice materials overall demonstrated a higher level of resistance compared to indica rice. The comprehensive index established in this study effectively reflects the resistance level of rice germplasms to bakanae disease at the seedling stage and has successfully identified two resistant germplasECEChese findings provide valuable insights for resistance identification and disease resistance breeding targeting rice bakanae disease.