Ilex verticillatais not only an excellent ornamental tree species for courtyards, but it is also a popular bonsai tree. ‘Oosterwijk’ and ‘Red sprite’ are two varieties ofIlex verticillata. The former has a long stem with few branches, while the latter has a short stem. In order to explain the stem growth differences between the two cultivars ‘Oosterwijk’ and ‘Red sprite’, determination of the microstructure, transcriptome sequence and IAA content was carried out. The results showed that the xylem thickness, vessel area and vessel number of ‘Oosterwijk’ were larger than in ‘Red sprite’. In addition, our analysis revealed that the differentially expressed genes which were enriched in phenylpropanoid biosynthesis; phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis in the black and tan modules of the two varieties. We found thatAST,HCTandbHLH 94may be key genes in the formation of shoot difference. Moreover, we found that the IAA content and auxin-related DEGsGH3.6,GH3,ATRP5,IAA27,SAUR36-like,GH3.6-likeandAIP 10A5-likemay play important roles in the formation of shoot differences. In summary, these results indicated that stem growth variations of ‘Oosterwijk’ and ‘Red sprite’ were associated with DEGs related to phenylpropanoid biosynthesis, phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis, as well as auxin content and DEGs related to the auxin signaling pathway.