X-ray absorption fine structure (XAFS) is a powerful tool to investigate electronic structures, valence states and molecular orientations at solid surfaces. In order to observe nano-scaled dynamic phenomena at solid surfaces, we have developed a micro-XAFS system using a photoelectron emission microscopy (PEEM) excited by synchrotron radiation in soft X-ray region. Here we explain the performance of our system concentrating on the recent development of quick measurements, and demonstrated that a PEEM image can be taken in a short time down to 10 msec. As an application of the system, we present the results for the real-time mapping of molecular orientations at nanometer scale for organic thin films. We demonstrated that the orientations of organic molecules in a microscopic region change during surface diffusion.