Layered transition metal compounds have attracted much attention due to their high theoretical capacity and energy density for sodium ion batteries. However, this kind of material suffers from serious irreversible capacity decay during the charge and discharge process. Here, using synchrotron-based operando transmission X-ray microscopy and high-energy X-ray diffraction combined with electrochemical measurements, the visualization of the dissymmetric phase transformation and structure evolution mechanism of layered NaNiO2 material during initial charge and discharge cycles are clarified. Phase transformation and deformation of NaNiO2 during the voltage range of below 3.0V and over 4.0V are responsible for the irreversible capacity loss during the first cycling, which is also confirmed by the evolution of reaction kinetics behavior obtained by the galvanostatic intermittent titration technique. These findings reveal the origin of the irreversibility of NaNiO2 and offer valuable insight into the phase transformation mechanism, which will provide underlying guidance for further development of high-performance sodium ion batteries.