Salinity and settleability are two major challenges for biological process in saline wastewater treatment. In this study, a pure marine bacterium Psychrobacter aquimaris X3-1403 (Ps. A. X3-1403) occupying good settleability was screened. Its self-flocculating mechanism and performance in saline wastewater treatment was explored. Results showed that extracellular polymeric substances (EPS) played an important role in the self-flocculating of Ps. A. X3-1403. Extracellular proteins contributed to the flocculation of 2.4 times that of extracellular polysaccharides. Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) analysis of EPS revealed that the amounts of hydrophobic functional groups were more than that of hydrophilic functional groups. Extracellular filamentous proteins played the key role in the initial particles formation of Ps. A. X3-1403. Then these small particles formed large and stable granules by the means of inter-micro-granule collisions, reconfiguration and hydrodynamic shear force. The increased cell surface hydrophobicity, particle size and specific gravity promoted the settleability of Ps. A. X3-1403. Moreover, Ps. A. X3-1403 demonstrated good treatment/settling performance in treating saline wastewater with different salinity. The application of this self-flocculating marine bacterium provide a successful case study of pure strain and expand the saline wastewater treatment processes.