This study aims to identify the relative Copy number variation (CNV) associated with the litter size of Dazu black goats based on the unpublished CNV analytical results of our previously published sequencing data, in which the litter-size groups were classified into extreme low- and high-yield groups. Firstly, to compare the existence of valuable CNV in Dazu black goats with different fertility levels with mixed pools. We obtained 4992 and 4888 CNVs from the HY and LY, which overlapping 1461 genes, and classified on the original CNV type. Three genes [LOC108633278, PPP1R12A, and YIPF4] were observed in the intersection between the HY deletion and the LY duplication groups. Secondly, on individuals level, we identified a novel candidate CNV (Chr1_50215501, FST = 0.148, VST = 0.347) from 214 autosomal credible CNVs to be significant with litter size in the Dazu black goat, which located in the CBLB gene. This finding indicates the CBLB gene may affect the litter size of the Dazu black goats through structural variations, and Chr1_50215501 can be an effective genetic marker for marker-assisted selection breeding, and this study was also helps understand the molecular mechanism related to the goat litter size.