The copper response of Proteus hauseri ZMd44 was determined using one-dimensional (1D) gel electrophoresis coupled with MALDI-TOF-TOF mass spectrometry for a similarity analysis of proteins isolated from P. hauseri ZMd44 cultured in CuSO4-bearing LB medium. Candidate proteins identified as a copper-transporting P-type ATPase (CTPP), phosphoenolpyruvate carboxykinase (PEPCK), flagellin (Fla), and outer membrane proteins (Omps) were the major copper-associated proteins in P. hauseri. In a comparative analysis of subcellular (i.e., periplasmic, intracellular, and inner membranes) and cellular debris, proteomics analysis revealed a distinct differential expression of proteins in P. hauseri with and without copper ion exposure. These findings were consistent with the transcription level dynamics determined using quantitative real-time PCR. Based on a genetic cluster analysis of copper-associated proteins from P. hauseri, Fla and one of the Omps showed greater diversity in their protein sequences compared to those of other Proteus species. Transmission electron microscopy (TEM) and the observed growth on LB agar plates showed that the swarming motility of cells was significantly suppressed and inhibited upon Cu(II) exposure. Thus, copper stress could have important therapeutic significance due to the loss of swarming motility capacity in P. hauseri, which causes urinary tract infections.