<p>The unconventional charge density wave (CDW) order in layered kagome lattice superconductors <i>A</i>V₃Sb₅ (<i>A</i> = K, Cs or Rb) triggers the emergence of novel quantum states such as time-reversal symmetry breaking and electronic liquid crystal states. However, atomic-scale manipulation and control of such phases remains elusive. Here we observe the emergent superconductivity and a primary pair density wave at the 2 × 2 Cs reconstructed surface of CsV₃Sb₅ by means of low-temperature scanning tunnelling microscopy/spectroscopy paired with density functional theory calculations. This quasi-two-dimensional kagome superconducting state with a critical temperature of ~5.4 K is intertwined with the bulk CDW order and exhibits a unique vortex core spectrum and a 4 × 4 pair density wave modulation of the superconducting gap. The emergent phenomena happen at a π-phase-shift dislocation in the periodicity of the CDW along the stacking direction if the 2 × 2 Cs superstructures are out of phase with the bulk CDW. Furthermore, we switched on and off the quasi-two-dimensional superconductivity through tip-assisted atomic manipulation of the 2 × 2 Cs superstructure. Thus, control of the surface reconstruction permits the creation, manipulation and control of quantum many-body states at antiphase boundaries in kagome lattice superconductors and, potentially, in other correlated materials.</p>