Sodium layered oxides with mixed transition metals have received significant attention as positive electrode candidates for sodium-ion batteries due to high reversible capacity. The larger ionic size and different bonding characteristics of Na ions exhibit distinctive electrochemical properties as compared to those for the lithium system. In particular, understanding structural changes by sodium extraction/insertion is considered to be a critical aspect for designing Na electrode materials. In situ XRD analysis is known to be an efficient way of relating electrochemical and structural properties of electrode materials, and to obtain detailed information about deintercalation/intercalation mechanisms during electrochemical cycling. Here we have developed a capillary based micro-battery cell, which allows us to obtain in situ information from the individual phases in the working battery. Through this approach, we carefully scrutinized a reversible structural phase transformation of the O3-layered material, NaFe0.5Co0.5O2, which is a promising positive electrode candidate for sodium-ion batteries by in situ synchrotron XRD investigation.