Ion migration in solids provides basis for a wide range of technique applications including alkali-metal ion batteries. Understanding the ion migration dynamics and kinetics is critical to bring benefits to the industry. Here, we directly track the Na ions insertion and extraction in van der Waals interactions dominated layered structure SnS2 at atomic-scale by in situ transmission electron microscopy technique. Insertion of sodium in SnS2 forms highly defective and expanded NaxSnS2 with volume expansion of (~5%) via a two-phase reaction while sodium extraction involves a solid solution behavior with formation of nano-sized intermediate superstructure Na0.5SnS2, of which the atomic structure has been identified to be row ordering in the (001) planes. The reaction behaviors of sodiation are also compared with lithiation in SnS2 nanostructures. Unlike the conversion and ionic bonded intercalation-type electrode materials, in this van der Waals material SnS2 the sodiation and lithiation reactions share great similarities in the dynamics (e.g. asymmetric reaction pathways). However, the high density of defects that are generated at the reaction front during sodiation, was not captured during lithiation probably due to the larger radius and heavy mass for Na ions. These findings provide valuable insights into understanding the underlying ion migration mechanism in the layered transition metal dichalcogenide. The asymmetric sodium insertion and extraction pathways may help us to elucidate the origins of voltage hysteresis and energy efficiency in alkali-metal ion batteries.