Somatic embryogenesis from nucellar tissues is common in many Zanthoxylum plants. The nuclear factor Y (NF-Y) transcription factor is pivotal in this process. Despite its significance, the identification and functional analysis of the NF-Y transcription factor family in Zanthoxylum armatum (Z. armatum) remains unexplored. This study identified 67 ZaNF-Y transcription factors in the diploid Z. armatum genome, comprising 20 ZaNF-YA, 30 ZaNF-YB, and 17 ZaNF-YC genes. Gene duplication, conserved domain, and motif analyses revealed the similarity and specificity of ZaNF-Y members in functional evolution. Cis-element analysis suggested that plant hormones and various transcription factor families may regulate ZaNF-Y gene expression, impacting nucellar embryo formation. Expression analysis across tissues indicated that the expression of most ZaNF-Y genes, such as ZaNF-YB5, was low in female flowers. In contrast, ZaNF-YC1 was highly expressed in female flowers and young fruit, indicating their potential role in nucellar embryo formation. Additionally, protein association network analysis provided insights into the composition of ZaNF-Y complexes. Our study enhances understanding of ZaNF-Y transcription factors and provides a basis for harnessing apomixis in hybrid crop production.