The α/β-type small acid soluble proteins (SASPs) are a major factor in protecting the spores from being killed in bacteria. In this article, we perform a systematic phylogenetic analysis of the α/β-type SASP in the genus of Geobacillus, which indicates that the whole family can be divided into three groups. We choose one protein from each group as a representative and construct the tertiary structure of these proteins. In order to explore the mechanism of protecting DNA from damage, 15 ns molecular dynamics simulation for the four complexes of Gsy3 with DNA are performed. The sequence alignment, model structure and binding energy analysis indicate that the helix2 region of SASPs is more conserved and plays a more crucial role in protecting DNA. Pairwise decomposition of residue interaction energies calculation demonstrate that amino acids of Asn10, Lys24, Asn49, Ile52, Ile56, Thr57, Lys58, Arg59 and Val61 take major effect in the binding interaction. The differences of energy contribution of the amino acids between different complexes make us conclude that the protein structure conformation has a slight change upon more proteins binding to DNA and consequently there occur protein-protein cooperation interactions.