In order to understand the molecular regulation of apomictic nucleolus development in walnuts, the apomictic kernels and fertilized kernels of ‘Xinxin 2’ walnut were used as the experimental materials in this study. The transcriptome and hormone contents such as indole-3-acetic acid (IAA), cytokinin (ZT), gibberellin (GA), brassinosteroid (BR), abscisic acid (ABA), and ethylene (ETH) were analyzed. The results showed that at 60 days after flowering, the contents of IAA, ZT, and BR in apomictic kernels were significantly (P<0.05) lower than those in normally fertilized kernels, decreasing by 28.57%, 19.59%, and 12.07%, respectively; the contents of GA, ABA, and ETH in apomictic kernels were significantly (P<0.05) higher than those in normally fertilized kernels, increasing by 34.91%, 31.50%, and 19.54%, respectively. At 80 days after flowering, the contents of IAA, ZT, and ETH in apomictic kernels were significantly (P<0.05) higher than those in normally fertilized kernels, increasing by 6.58%, 17.80%, and 7.44%, respectively; meanwhile, the contents of GA, BR, and ABA in apomictic kernels were significantly (P<0.05) lower than those in normally fertilized kernels, decreasing by 29.37%, 14.99%, and 10.65%, respectively. At 100 days after flowering, the contents of IAA, ZT, GA, BR, and ETH in apomictic kernels were significantly (P<0.05) higher than those in normally fertilized kernels, increasing by 18.87%, 30.12%, 16.96%, 3.70%, and 20.57%, respectively; the content of ABA in apomictic kernels was significantly (P<0.05) lower than those in normally fertilized kernels, decreasing by 44.85%. Transcriptome sequencing result showed that 62 differentially expressed genes (DEGs) involved in plant hormone signal transduction pathways were identified. Among them, auxin influx carrier gene (AUX1 LAX_2), B-class cytokinin response factor gene (ARR-B1), abscisic acid receptor gene (PYL2), BAK family gene (BAK1), and phosphotransferase gene (AHP4) were upregulated in apomictic kernels, whereas F-box protein gene (GID2_SLY1_2) and E3 ubiquitin ligase genes (EBF1/2_1, EBF1/2_2) were downregulated. Eight genes that related to differentially metabolites were verified by qRT-PCR and the results were consistent with the finding in transcriptome analysis. It was concluded that during the oil conversion period of walnuts, high contents of IAA, ZT, BR, ETH could promote the development of apomictic kernels. Genes such as AUX1 LAX_2, ARR-B1, PYL2, BAK1, AHP4, GID2_SLY1_2, and EBF1/2 which connect with plant hormone signal transduction pathways were participating in regulating the development of apomictic kernel development.