This study estimated the genetic parameters affecting the body weight trait of Litopenaeus vannamei juveniles under low-temperature fluctuation, using the 40K SNP genotyping information of L. vannamei, with the aim of providing fundamental data for the breeding of new L. vannamei varieties tolerant to low temperatures. A total of 4000 L. vannamei juveniles from 40 families were used in a culture experiment. The culture temperature was reduced from 30 ℃ to 20 ℃ by the addition of underground well water, and then stabilized for 4 days after 24 h of natural warming. Continuous cultivation was conducted for 15 days after the cooling-warming-stabilizing process had been repeated 3 times, and the body weight and survival traits of the juveniles were then measured. Compared with that in the control group, low-temperature fluctuation had a significant effect on the growth of L. vannamei larvae (P＜0.05) but not on the survival traits (P＞0.05). An A-matrix was constructed based on individual genealogical information, and the 40K SNP chip was used for SNP genotyping of 159 parents and their SIB individuals. An H-matrix was constructed by combining SNP and pedigree information, estimation of variance components, and the genetic parameters of body weight traits using individual animal models. According to the Aand H-matrices, respectively, the heritability of body weight was 0.37±0.07 and 0.40±0.08 for L. vannamei larvae under low-temperature fluctuation, indicating a high heritability level. This cross-validation shows that there is no significant difference in prediction accuracy and bias between the two matrices. The body weight of L. vannamei under low-temperature fluctuation showed abundant genetic variation, indicating that multi-generation breeding may result in notable genetic gain.