As a signal molecule, hydrogen sulfide (H2S) plays an important role in plant growth. In this study, the effect of different concentration of H2S donor, sodium hydrosulfide (NaHS), on growth of tomato seedlings was tested in hydroponic culture. The effects of 50 μM NaHS on tomato seedlings were not significant, compared with the control. After 100 μM NaHS treatment, plant height, shoot fresh weight and dry weight increased significantly. However, 300, 500 and 1000 μM NaHS had inhibitory effect on tomato seedlings, especially 1000 μM NaHS. 100 μM NaHS could increase chlorophyll a, chlorophyll b, and total chlorophyll content, stomatal conductance, net photosynthetic rate, transpiration rate and intercellular CO2 concentration. The activities of nitrate reductase, glutamate synthase and glutamine synthase, and L-cysteine demethylase (LCD), and nitrate content, were increased significantly after 100 μM NaHS treatment. The microarray results showed that 9122 genes changed after treated with 100 μM NaHS for 3 h, and 430 genes changed more than 2 times. These genes were grouped into metabolism, signal transduction, stress resistance, transcription factors, transport, protein synthesis and degradation, hormone response, and cell wall related genes in tomato seedlings. RT-PCR analysis showed that the expression of some MAPK family genes changed significantly when exogenous NaHS was added, especially SlMAPK3 and SlMAPK13. The MAPK inhibitor PD98059 reduce the LCD activity and H2S content in tomato seedlings, which indicated that MAPK signaling pathway was involved in the process of H2S promoting tomato seedling growth.