Low-level vancomycin-resistant S. aureus designated as heterogeneous vancomycin-intermediate S. aureus (hVISA) have been associated with treatment failure and unable to detect by routine disk diffusion method. As small angle X-ray scattering (SAXS) can be used for studying size, shape, and biology structure of bacterial cells; thus, this study aimed to investigate the SAXS patterns of biomolecules of vancomycin susceptible S. aureus (VSSA), hVISA, and, VISA cells. A total of 9 S. aureus isolates, 3 each from VSSA, hVISA, and VISA groups, were cultured on brain heart infusion agar with and without vancomycin. The cultured cells were kept overnight to reach their exponential phase and subjected to the SAXS using beamline 1.3W: SAXS. Under vancomycin untreated condition, the VISA cells showed different SAXS pattern from those of the VSSA and the hVISA, whereas the vancomycin treated cells of hVISA and VISA displayed similar SAXS patterns. The ribosome of VSSA was significantly smaller than that of hVISA under the untreated condition but showed no statistically different under the treated condition. In addition, when compared the ribosome and the DNA of VSSA with the VISA's and the DNA of VISA with the hVISA's, they were different only under the untreated condition. This preliminary study showed that under the stress condition mediated by vancomycin, the vancomycin non-susceptible S. aureus (hVISA and VISA) had similar SAXS patterns; while under the non-stress condition, the VSSA and hVISA showed similar patterns. This study provides preliminary information on bacterial adaptation under vancomycin-mediated stress condition.