The NAC transcription factor is a peculiar kind of transcription factor in plants. Transcription factors are involved in the expression of plant genes under different conditions, and they play a crucial role in plant response to various biotic and abiotic stress. We transferred the ClNAC9 gene into Chrysanthemum grandiflora ‘niu9717’ by Agrobacterium tumefaciens–mediated transformation. The results of kanamycin-resistant screening, polymerase chain reaction (PCR) detection, and Northern blot analysis proved that the target gene had been integrated into the genome of the target plants. Wild-type (WT) plants and transgenic plants were treated with different concentrations of NaCl, NaHCO3, and drought stress, and physiological indexes, such as antioxidant system activity (superoxide dismutase, peroxidase, catalase), malondialdehyde accumulation, and leaf relative water content, were measured. We also observed changes in plant morphology. The physiological indexes’ changing range and extreme values suggested that transgenic plants’ resistance to salinity, alkali, and drought stress was significantly higher than WT plants. Transgenic plant growth was less inhibited compared with WT plants, indicating that the ClNAC9 gene increased the resistance of transgenic plants under the stress of salinization, alkalization, and drought.