Stenotrophomonas maltophilia is an important multidrug-resistant pathogen that utilizes diverse two-component systems (TCSs) to regulate its physiological functions. However, the regulatory roles of the SmaSR TCS remain poorly understood. We constructed SmaSR proteins deletion (D7677) and overexpression (O7677) strains of S. maltophilia CYZ, and performed proteomics to identify the changes of expression levels of differentially expressed proteins.