Abstract: The present disclosure provides a genomic selection (GS) breeding chip of Huaxi cattle and use thereof, and relates to the technical field of molecular breeding. The present disclosure provides a molecular marker combination for whole-genome genotyping of Huaxi cattle, where a genotyping object involves 112,177 single nucleotide polymorphisms (SNPs) and 3 Indels, including seven marker panels in total. In the present disclosure, a genome-wide breeding chip constructed with the molecular marker combination has functional relevance, pertinence and effectiveness, innovation, comprehensiveness, practicality, and cost-effectiveness. This breeding chip also shows uniform distribution of chromosomes in the whole-genome, high coverage, and moderate throughput of markers. This breeding chip has desirable compatibility with existing commercial chips and high cost performance.