Banana (Musa sp.) is one of the world’s most important crops, and a source of extreme economic importance in many countries around the world. However, the height of banana plant poses a significant challenge in both harvesting fruit and their tolerance to extreme weather. Gibberellin (GA) is one of the important endogenous hormones affecting plant height. Copalyl diphosphate synthase (CPS) is the first key enzyme in the GA biosynthesis pathway. In this paper, two full-length coding sequences of CPS genes were cloned from ‘William B6’ dwarf mutant banana and its wild-type parent (Musa AAA group), named CPS-A and CPS-G, respectively. The full-length complementary DNA (cDNA) sequences of CPS-G and CPS-A were both 2163 base pairs (bp), and encoded 720 amino acid residues. There were eight differences between the two speculative amino acid sequences in the alignment analysis. The molecular weights of CPS-G and CPS-A were 82,359.00 and 82,412.15 Da, respectively, and their isoelectric points were 6.17 and 6.03, respectively; there were no signal peptides and transmembrane structures. The banana CPS was mainly located in the cytoplasm by subcellular localization prediction. The results of reverse quantitative real-time polymerase chain reaction showed that CPS gene expression levels in the leaves and false stems of dwarf banana were lower than those of wild banana except for the developmental stage of the 10th leaf. Its expression level in the dwarf banana stem was significantly lower than that of the wild type at the 15th, 20th, and 25th-leaf age, respectively. The results showed that the dwarfism of the ‘Williams B6’ dwarf mutant might be related to the mutation of the CPS sequence and the difference of expression level. This study laid a foundation for further research on functional verification and the genetic regulation mechanism of the CPS gene.