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Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida. [ABSTRACT FROM AUTHOR]