Abstract: To clarify the relationship between the expression levels of innate immune molecules in the grass carp (Ctenopharyngodon idella) broodstock and the disease resistance of their progeny, this study used techniques such as ELISA and Western blot to measure the expression levels of innate immune molecules (C3, Bf, MBL, and LZM) in the plasma of 585 original Yangtze C. idella broodstock. Based on differences in immune molecule levels, the C. idella broodstock were grouped, and the disease resistance of progeny from parents with different immune levels was evaluated through viral infection and aquaculture comparison experiments. The results showed that the scatter plots of C3, Bf, LZM, and MBL expression levels in the original Yangtze C. idella broodstock were similar in shape and generally conformed to a normal distribution, indicating diversity in the expression levels of innate immune molecules in the Yangtze C. idella broodstock population. Based on the comprehensive expression levels of these four innate immune molecules, the Yangtze C. idella broodstock were divided into Group A (top 20%), Group B (middle 20%–80%), and Group C (bottom 20%), and their progeny were obtained through within-group breeding. C. idella reovirus infection experiments revealed that the survival rate of Group B C. idella progeny after infection was more than doubled compared to those of Group B and Group C. In aquaculture comparison experiments, the feed conversion ratio and specific growth rate of Group B C. idella progeny were superior to those of ordinary C. idella progeny, with higher total aquaculture yield and survival rates. This study confirms the diversity in the expression levels of innate immune molecules in the original Yangtze C. idella broodstock. Selecting broodstock with moderate levels of innate immune molecules can produce progeny with stronger disease resistance and better growth traits, providing a new theoretical basis and technical approach for disease-resistant breeding in C. idella.