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Jujube production is threatened by jujube witches’ broom (JWB) disease, which is caused by JWB phytoplasma. The jujube TCP transcription factor (TF) <i>ZjTCP16</i> may be involved in the interaction of jujube plants with JWB phytoplasma. In this study, qRT-PCR proved that the expression pattern of <i>ZjTCP16</i> was altered by JWB phytoplasma. The gene functions of <i>ZjTCP16</i> were analyzed by its overexpression in <i>Arabidopsis</i> and jujube, as well as knock-down in. The overexpression of <i>ZjTCP16</i> in <i>Arabidopsis</i> and jujube resulted in dwarfism and small leaves, while the <i>zjtcp16</i> CRISPR mutants were higher than the WT. Microscopic observation of paraffin sections of jujube stems showed that <i>ZjTCP16</i> affected the size of cells. The interactions of ZjTCP16 with ZjAS2 and ZjLOB in both the cytoplasm and nucleus were demonstrated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Yeast one-hybrid (Y1H) assays and qRT-PCR further confirmed that <i>ZjTCP16</i> affected the expression of genes involved in leaf morphogenesis and cell proliferation (<i>ZjAS1</i>, <i>ZjKNAT1</i>, <i>ZjKNAT2</i> and <i>ZjKNAT6</i>) at the mRNA level through the ZjAS2 and ZjLOB pathways. In conclusion, <i>ZjTCP16</i> regulates plant growth and cell size by altering the expression pattern of morphogenesis-related genes in jujube.