The breeding array is currently the most popular genotyping tool and has played an important role in crops and livestock breeding. In the aquaculture industry, many genotyping arrays have been developed and applied to the genetic breeding of important aquaculture species. The large yellow croaker (Larimichthys crocea) industry in China is threatened by numerous problems, such as germplasm degradation and frequent diseases. It is urgent to overcome the current development bottleneck through breeding, and a stable breeding array is needed. In this study, a breeding array named “Ningxin-2” is developed based on the high-throughput single nucleotide poly-morphism (SNP) array “Ningxin-1.” The “Ningxin-2” array selects representative SNP sites in the haplotype block of large yellow croakers and integrates SNP sites that are associated with cryptocaryon resistance and high-temperature tolerance of the large yellow croaker. The “Ningxin-2” breeding array integrates 54077 high-quality SNP sites evenly distributed in the large yellow croaker genome. Evaluation of “Ningxin-2” in 756 large yellow croakers from six populations shows that the call rate of the array is above 98.4%, and the proportion of polymorphic SNP is above 91.2%. The “Ningxin-2” is stable, accurate, and cost-efficient, and it is expected to play an important role in research for targeted genetic improvement and genomic selection of large yellow croakers.