The relationship between plant growth and abiotic stress resistance is a subject of concern in plant science, which is of great significance for crop genetic improvement. In this study, a ZFHD TF, T. HALOPHILA HOMEOBOX PROTEIN 1(TsHD1), was identified as the partner of TsNAC1 TF, and cloned from the halophyte Thellungiella halophila. TsHD1 is a homeodomain (HD) transcription factor and functions as a collaborator of TsNAC1. TsHD1 can form heterodimers with TsNAC1 via the interaction between its zinc finger (ZF) domain and the A subdomain of TsNAC1. The overexpression of TsHD1 improved the heat stress resistance of T. halophila and retarded its vegetative growth slightly. The co-overexpression of TsHD1 and TsNAC1 highly improved heat and drought stress resistance by increasing the accumulation of heat shock proteins and enhancing the expression levels of drought stress response genes, such as MYB DOMAIN PROTEIN 77 and MYB DOMAIN PROTEIN 96 (MYB77and MYB96) and SALT TOLERANCE ZINC FINGER 10 and SALT TOLERANCE ZINC FINGER 18 (ZAT10 and ZAT18), but seriously retarded the vegetative growth of T. halophila by restraining cell expansion. The heterodimer of TsHD1 and TsNAC1 has higher transcriptional activation activity and higher stability compared with the homodimer of TsHD1 or TsNAC1. The binding sites of the TsHD1 and TsNAC1 heterodimers were found to exist in the promoters of most upregulated genes in Cauliflower mosaic virus 35S promoter (P35S)::TsHD1 and P35S::TsNAC1 transgene lines compared with the wild type using RNA-seq and genomic data analyses. Moreover, the binding sites in the promoter region of the most downregulated genes were located in the vicinity of the TATA-box. This study reveals that TsNAC1 and TsHD1 play roles in plant growth and abiotic stress resistance synergistically, and the effects depend on the heterodimer binding to the specific target sites in the promoter region.