Characterizing　interactions　between　microbial　cells　and　their　specific　inhibitory　drugs　is　essential　for　developing　effective　drugs　and　understanding　the　therapeutic　mechanism.　Functional　metal　nanoclusters　can　be　effective　inhibitory　agents　against　microorganisms　according　to　various　characterization　methods,　but　quantitative　three-dimensional　(3D)　spatial　structural　analysis　of　intact　cells　is　lacking.　Herein,　using　coherent　X-ray　diffraction　imaging,　we　performed　in　situ　3D　visualization　of　unstained　Staphylococcus　aureus　cells　treated　with　peptide　mineralized　Au-cluster　probes　at　a　resolution　of　similar　to　47　nm.　Subsequent　3D　mass-density　mapping　and　quantitative　structural　analyses　of　S.　aureus　in　different　degrees　of　destruction　showed　that　the　bacterial　cell　wall　was　damaged　and　cytoplasmic　constituents　were　released　from　cells,　confirming　the　significant　antibacterial　effects　of　the　Au-cluster　probe.　This　study　provides　a　promising　nondestructive　approach　for　quantitative　imaging　and　paves　the　way　for　further　research　into　microbe-inhibitor　drug　interactions.