Rice–crab co-culture systems represent integrated agriculture–aquaculture systems developed in China over the last 30 years. The rice–crab co-culture area comprised approximately 1.386 × 10⁵ hm² in 2019. However, there is no specific feed designed for Chinese mitten crab (Eriocheir sinensis) cultured in this system until now. In this study, we investigated feed formulae for the nutritional requirements of Chinese mitten crab in this mode. The control group was not fed with any artificial feed (Co), and the experimental groups were fed with three different feeds of 15% (T15), 30% (T30), or 45% (T45) protein content, respectively. Growth performance variations in E. sinensis were investigated along with water quality, phytoplankton, zooplankton, aquatic vascular plants, and benthic animals in the paddy fields to determine the effect of crabs and their diet on the paddy ecosystem. Dietary protein levels had no significant effect on water quality. The biomass and species of phytoplankton, zooplankton, aquatic vascular plants, and zoobenthos in the paddy field were affected by crabs and their diet. Morphological parameters of crabs were significantly more pronounced in the high-protein group than in the other groups. However, the T45 diet negatively affected production by increasing feed costs, causing precocious puberty and inducing water eutrophication. In conclusion, adding a 15% protein compound feed can meet the nutritional needs of crabs, reduce culture costs, and improve water quality. The discharged water had low ammonia nitrogen and nitrite content and no eutrophication occurred, so the water could be recycled. These findings provide a scientific reference for supporting rice and fish co-cultivation.

“Milky disease” of the Chinese mitten crab (Eriocheir sinensis), caused by Metschnikowia bicuspidata, leads to substantial economic losses. Despite extensive research on its pathogenesis, the genetic basis of host resistance and underlying regulatory mechanisms remain unclear, limiting the development of disease-resistant varieties. This study aimed to (1) evaluate resistance differences among 10 E. sinensis families (five highly resistant and five sensitive) via artificial challenge; (2) identify disease-resistance-associated genetic loci using genome-wide association analysis (GWAS). Our findings revealed that the F05 family exhibited the strongest resistance, with a mortality rate of only 3% and a molting rate of 73%, accompanied by superior growth performance. Whole-genome resequencing identified 10,161,545 high-quality SNPs, and GWAS detected 767 loci significantly associated with disease-resistance traits, among which two pleiotropic SNPs (Chr46:18395778 and Chr1:20680490) were simultaneously associated with both “dead or not” and “qPCR fixed amount of fungi”, reflecting their functional relevance in regulating survival and pathogen load. Notably, we propose for the first time that E. sinensis achieves resistance by inducing M. bicuspidata into a viable but nonculturable (VBNC) state, in which the fungal cells remain metabolically active but cannot form colonies on conventional culture media. This study establishes a multidimensional resistance evaluation system, clarifies the genetic basis and novel mechanism of resistance, and provides valuable molecular markers for marker-assisted breeding. The findings contribute to reducing disease-related losses and promoting sustainable development of the E. sinensis aquaculture industry.