To optimize the multi-trait synergistic breeding strategy for Marsupenaeus japonicus, this study was based on a G3 selected population. Twenty-eight full-sib/half-sib G4 families were constructed through fluorescent marker mixed culture and natural mating. A combination of linear mixed and generalized linear models was used to systematically evaluate genetic parameters of body length, body weight, and ammonia nitrogen tolerance traits at 120, 180, and 240 days of age, and to assess genotype-environment interaction effects under indoor and outdoor conditions. The results showed that growth traits exhibited moderate heritability, with body length ranging from 0.2992 to 0.4390 and body weight from 0.1324 to 0.3718. The heritability of ammonia nitrogen tolerance traits was low, ranging from 0.0914 to 0.1731. Genetic (0.8501~0.9145) and phenotypic (0.9001~0.9819) correlations between growth traits at different ages were all extremely significantly positive (P < 0.01), indicating that early selection can simultaneously improve phenotypes across multiple growth stages. Genetic correlations between growth and ammonia nitrogen tolerance traits ranged from –0.1957~0.0362 and those between growth and phenotypic correlations ranged from –0.0975~0.0955, with neither being significant (P>0.05), thereby suggesting regulation by independent genetic mechanisms. Genetic correlations of body length and body weight traits between indoor and outdoor environments were –0.017±0.176 and 0.136±0.185, respectively, both<0.8, indicating significant genotype-environment interaction effects on M. japonicus body length and body weight under different breeding conditions. Therefore, to achieve simultaneous improvement of growth and ammonia nitrogen tolerance traits, breeding values for both traits should be estimated, while a comprehensive selection index calculated to realize multi-trait synchronous improvement. Meanwhile, different breeding schemes should be tailored to specific indoor and outdoor breeding environments. The findings of this study provide a theoretical basis for designing efficient breeding programs for M. japonicus.