Changfeng silver carp (Hypophthalmichthys molitrix) is a new variety of silver carp bred by the Yangtze River Fisheries Research Institute of the Chinese Academy of Fishery Sciences. It has many advantages, such as a quick growth rate, a high body size, and a neat appearance, which are associated with more excellent growth characteristics than those of common H. molitrix. And growth traits are important economic traits of aquaculture species. However, the study on H. molitrix at home and abroad mainly focuses on developing microsatellite markers, analyzing genetic structure, and establishing the genetic linkage map. Few molecular markers associated with H. molitrix growth traits have been considered, and it is not known whether these markers can be used in the selection and breeding of Changfeng H. molitrix. This study aimed to screen out the molecular markers related to the growth traits of Changfeng H. molitrix to guide the germplasm identification and selective breeding. In this study, 15 polymorphic microsatellite markers were used to analyze the genetic diversity and growth trait association of Changfeng H. molitrix at 6, 17 and 36 months. The results show that a total of 51 alleles were detected at 6 months, and the average number of alleles was 3.40; a total of 42 alleles were detected at 17 months, and the average number of alleles was 2.80; A total of 46 alleles were detected at 36 months, and the average number of alleles was 3.07. The observed heterozygosity (H_o) and expected heterozygosity (H_e) of each month-old group Changfeng H. molitrix were higher than 0.5. The average PIC values were 0.555, 0.445, and 0.490 respectively at each age; indicating that the population was highly genetically diverse. The results of associations between microsatellite markers and growth traits revealed that locus BL55 and BL109 were significantly associated with body height at 6-month-old (P<0.05); S65 was found significantly associated with body height at 17-month-old (P<0.05); locus BL55 was significantly associated with total length (P<0.05), and BL106-2 and BL116 were significantly associated with body weight at 36-month-old (P<0.05). The different growth traits associated with different months of age of the same marker may be due to the different growth trends of Changfeng H. molitrix. Locus BL55 on chromosome 15 has the same allele containing DNA fragment length of 231 bp at different month ages, and it is preliminarily speculated that the genotypes 225/231, and 231/245, will have negative and positive effects, respectively. To further examine whether this locus can be used for molecular marker-assisted breeding in H. molitrix populations, two wild populations of H. molitrix from Yangtze River and Xiangjiang were selected for analysis. The results showed that the allele of the 231 bp fragment existed in both the Yangtze River and Xiangjiang populations. This result preliminarily confirmed that the marker BL55 was determined as a candidate marker related to growth traits, which has reference value for genetic improvement and selective breeding of H. molitrix.