Background: Considering the twin global problems of increasingly serious energy shortage and effects of salt stress on biofuel plants, breeding of salt-resistant biofuel plant and the discovery of mechanisms for biomass accumulation under salt stress is necessary for energy shortage. Proso millet (Panicum miliaceum L.) is very resilient to abiotic stress, especially to land degradation caused by soil salinization, and its promising as dedicated bioenergy crops for the production of renewable fuels and forage, due to its high photosynthetic efficiency C4 plant and ability to grow in a range of environmental conditions. However, the mechanisms by which the roots of proso millet adapt and tolerate salt-stress are obscure.Results: In this study, plants of a salt-sensitive cultivar (SS 212) and a salt-tolerant cultivar (ST 47) of proso millet were exposed to severe salt stress and subsequent re-watering. ST 47 exhibited greater salt tolerance and faster recovery than SS 212, as evidenced by higher increases in total root length (TRL), root surface area (RSA), root tip number (RTN), biomass. Moreover, microstructural analysis showed that relative to SS 212, the roots of ST 47 could maintain more intact internal structures, and thicker cell wall under salt stress, thereby stronger resistance to salt toxicity and maintenance of growth. Digital RNA sequence analysis suggested more genes involved in salt stress resistance were induced in ST 47 than in SS 212. In ST 47 also, re-watering restored most genes that had been induced by salt stress. Results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis revealed that ST 47 maintained better Na+/ K+ balance to resist Na+ toxicity via a higher capability to restrict Na+ uptake, vacuolar Na+ sequestration, and Na+ exclusion. The mechanism for cell wall biosynthesis in cultivar ST 47 involved the promotion of cell wall composition changes, via efficient regulation of galactose metabolism and biosynthesis of cellulose and phenylpropanoids. Conclusions: Overall, this study provides valuable salt-resistant biofuel resources and mechanisms for relieving the world energy shortage, which could be applied for the rehabilitation of saline lands.