Transition metal sulfides are promising high-capacity anode materials for sodium ion batteries in terms of the conversion reaction with multiple electron transfers. Nonetheless, some inherent challenges such as sluggish sodium ion diffusion kinetics, large volume change and poor cycle stability limit their implementation. Addressing these issues necessitates a comprehensive understanding on the complex sodium ion storage mechanism especially at the initial cycle. Here, taking nickel subsulfide as a model material, we reveal the complicated conversion reaction mechanism upon the first cycle by combining in operando 2D transmission X-ray microscopy with X-ray absorption spectroscopy, ex-situ 3D nano-tomography, high-energy X-ray diffraction and electrochemical impedance spectroscopy. This study demonstrates that the microstructure evolution, inherent slow sodium ion diffusion kinetics, and slow ion mobility at the two-phase interface contribute to the high irreversible capacity upon the first cycle. Such understandings are critical for developing the conversion reaction materials with the desired electrochemical activity and stability.