Two-dimensional (2D) transition-metal dichalcogenides hold enormous potential for applications in electronic and optoelectronic devices. Their distinctive electronic and chemical properties are closely related to the structure and intercalation chemistry. Herein, the controversial phase transition from semiconductive 2H to metallic 1T phase and occupancy of the intercalated sodium (Na) upon electrochemical Na intercalation into MoS2 are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope. In addition, a series of other complicated phase transitions along with lattice distortion, structural modulation, and even irreversible structural decomposition are recognized in MoS2 depending on the content of Na ion intercalation. It is shown that x = 1.5 in Na(x)MoS2 is a critical point for the reversibility of the structural evolution. Our findings enrich the understanding of the phase transitions and intercalation chemistry of the MoS2 and shed light on future material design and applications.