Seed dimorphism provides plants with alternative strategies for survival in unfavorable environments. Here, we investigated the physiological responses and differential gene expression caused by salinity exposure in Atriplex centralasiatica plants grown from the two different seed morphs. Seedlings derived from yellow seeds (YS) showed a greater salt tolerance than those derived from brown seeds (BS). Salt treatment induced nitric oxide (NO) synthesis in roots, and seedlings derived from YS produced greater amounts of NO than did those from BS. Analyses of NO scavenging during salt stress revealed that NO contributed to the differential salt tolerance in seedlings derived from the two seed morphs by modulating antioxidative enzyme activity, hydrogen peroxide accumulation and the ion equilibrium. We also applied transcriptomics and subsequent microarray analysis to evaluate the differential gene expression during salt treatment. These genes encoded proteins related to osmotic and ionic homeostasis, redox equilibrium and signal transduction. A select group of genes including GH3.3, CAT1/2, TIP1, SIHP1 and EXP1 were further confirmed with RT-PCR analysis. These results revealed that the enhanced salt tolerance of seedlings from YS appeared to be governed by a superior ability to achieve ionic homeostasis and redox equilibrium, a rapid response to salt stress, and ultimately better growth potential. NO serves as a vital regulator in these processes.