Increasing temperature extremes are caused by global climate change. Extreme low temperature has caused the increase of death rate for Nibea albiflora in winter, which has seriously restricted the development of aquaculture industry. N. albiflora is one of the important mariculture fish in China. Studying the molecular mechanism of response to low temperature stress can provide theoretical basis for N. albiflora culture to cope with the challenges of extreme low temperature. In this study, 200 N. albiflora individuals were selected to low-temperature stress at 5 °C, and the survival time, weight, body length, sex and other phenotypic parameters of every individual were recorded. Then, whole genome was resequenced. A total of 3 005 715 high-quality single nucleotide polymorphism (SNPs) sites were obtained by comparing to the reference genome (NCBI GenBank number: GCA_014281875.1), and the obtained SNP sites were used for genome-wide association analysis (GWAS) using the Mixed linear model (MLM) based on EMMAX software. The results showed that the phenotypic parameters such as body weight, body length and sex were not significantly correlated with the low temperature tolerance time (P=0.834-0.013). However, 9 sites were identified on 24 chromosomes that were significantly correlated (P=1.98×10^-6- 4.61×10^-8) with the low temperature tolerance time, and a total of 13 candidate genes, such as CBL.3, STOML2.2 and SLC37A3 were annotated. Gene ontology (GO) analysis showed that the above genes were mainly enriched in the processes of immunity, defense and repair, stress and mitochondrial energy metabolism, which may be related to low temperature response of the N. albiflora. The results of this study can provide reference for the genetic improvement of low temperature tolerance.