Among the III-nitride semiconductors, InxGa1-xN is a key material for visible optical devices such as light-emitting diodes (LEDs), laser diodes, and solar cells. Light emission is achieved via electron-hole recombination within the InxGa1-xN layer. When InxGa1-xN-based blue LEDs were first commercialized, the high probability of electron-hole radiative recombination despite the presence of numerous threading dislocations was a mystery. Extensive studies have proposed that carrier localization in nanoscopic potential fluctuations due, for example, to the immiscibility between InN and GaN or random alloy fluctuations is a key mechanism for the high emission efficiency. In actual LED devices, not only nanoscopic potential fluctuations but also microscopic ones exist within the InxGa1-xN quantum well light-emitting layers. Herein we map the synchrotron radiation microbeam X-ray fluorescence of InxGa1-xN blue LEDs at a sub-micron level. To acquire weak signals of In, Ar, which is in the air and has a fluorescent X-ray energy similar to that of In, is evacuated from the sample chamber by He purge. As a result, we successfully visualize the spatial In distribution of InxGa1-xN layer nondestructively and present good agreement with optical properties. Additionally, we demonstrate that unlike nanoscopic fluctuations, microscopic In compositional fluctuations do not necessarily have positive effects on device performance. Appropriately controlling both nanoscopic and microscopic fluctuations at the same time is necessary to achieve supreme device performance.