Ferromagnetism in two-dimensional (2D) materials provides an ideal platform to study emergent electromagnetic phenomena in low dimensions for future spintronics. In magnetic-element intercalated transition metal dichalcogenides, topologically nontrivial spin textures, such as chiral helimagnetic spin states and chiral soliton lattices, are realized due to the chiral lattice distortions induced by intercalated magnetic ions. Consequently, the magnetic chirality is predictably determined by the sign of antisymmetric exchange interaction (or Dzyaloshinskii–Moriya interaction, DMI) vector that is coupled to the underlying crystal chirality. Here, using cryogenic Lorentz phase microscopy, we directly observed the chirality reversal behavior of the chiral soliton lattices in Cr1/3TaS2 across the structural defects. We show that a partial 1 T stacking in 2H-TaS2 locally reduces DMI, leading to magnetic chirality reversal with direct atomic resolution imaging. Our experimental results show that manipulation of stacking sequence provides a viable way to control the chirality of topologically nontrivial soliton lattices in 2D magnets.