Chromosome segregation is regulated by the ParABS system that is an important biological process in all domains of life. ParABS system includes ParA (an ATPase), ParB (a parS binding protein) and parS (a centromere-like dsDNA). The homologous proteins of ParA and ParB in Helicobacter pylori are HpSoj and HpSpo0J, respectively. We characterized the binding of parS and HpSpo0J and solved the crystal structure of the HpSpo0J-parS complex, with two HpSpo0J molecules bind with one parS. HpSpo0J interacts vertically and horizontally with its neighbors through the N-terminal domain to form an oligomer. These adjacent and transverse interactions might be needed for molecular assembly of a high order nucleoprotein complex and for ParB spreading. In addition, the ATPase activity of HpSoj was determined and the non-specific DNA binding of HpSoj dimer was detected. Based on these findings, we propose a structural model for the HpSoj and HpSpo0J complex in the ParABS partitioning system.