Elemental surface topography information in microscopic material characterization contributes to a better understanding of surfaces, interfaces, substrates, and their applications. Here, a general approach based on microbeam proton-induced X-ray emission (micro-PIXE) to reconstruct the three-dimensional (3D) elemental surface topography using the annular multisegment silicon drift detector has been demonstrated. The proposed method includes four main steps: acquiring four two-dimensional elemental concentration maps using the multichannel spectrometer, reconstructing the local inclination angle from the atomic model of ion–matter interaction, calculating the two independent topography gradient components, and numerical surface topography integration. In this study, the general algorithm to obtain the gradient components has been successfully tested on a four-segment configuration to reconstruct the 3D surface topography of compound alloys with different microstructure scales. In synchrotron and accelerator facilities dealing with elemental X-ray mapping where the development of customized multisegment detectors is needed, the introduced method is applicable to elemental surface/interface roughness reconstruction in microscale for cultural heritage samples, fusion plasma-facing materials, and microelectronic devices.