Stenotrophomonas maltophilia is an important opportunistic pathogen that utilizes SmeE efflux pump to extrude structurally dissimilar antibiotics. Here, we constructed smeE gene deletion (D531) and overexpression (O531) strains of S. maltophilia CYZ, and investigated changes in biological functions by analyzing the transcriptional and expression levels of differentially expressed genes and proteins, respectively. S. maltophilia D531 showed significant susceptibility to erythromycin, quinolones, and tetracycline. The organism exhibited stronger bacterial motility, which was due to the upregulated expressions of FlhA and MotB proteins. Because the expression levels of SM01853, OhrB, DnaK, GrpE, and HslJ proteins were downregulated, S. maltophilia D531 increased susceptibilities to H2O2 and high temperature. Conversely, S. maltophilia O531 exhibited resistance to H2O2 and high temperature and enhanced biofilm-forming capacity, since the expressions of KatE, SM02481, PilO and PilQ proteins in S. maltophilia O531 were upregulated. However, both S. maltophilia D531 and O531 reduced tolerance towards Zn2+, and the expression of Zn transporter was found to be downregulated. Additionally, it is necessary to demonstrate whether downregulation of SmeN and SM02901 proteins resulted in S. maltophilia O531 reduced resistance to aminoglycosides. The current study may give important leads in elucidating the changes in biological functions via transcriptomic and proteomic analyses.