Phonon polaritons (PhPs) have attracted significant interest in the nano-optics communities because of their nanoscale confinement and long lifetimes. Although PhP modification by changing the local dielectric environment has been reported, controlled manipulation of PhPs by direct modification of the polaritonic material itself has remained elusive. Here, chemical switching of PhPs in α-MoO3 is achieved by engineering the α-MoO3 crystal through hydrogen intercalation. The intercalation process is non-volatile and recoverable, allowing reversible switching of PhPs while maintaining the long lifetimes. Precise control of the intercalation parameters enables analysis of the intermediate states, in which the needle-like hydrogenated nanostructures functioning as in-plane antennas effectively reflect and launch PhPs and form well-aligned cavities. We further achieve spatially controlled switching of PhPs in selective regions, leading to in-plane heterostructures with various geometries. The intercalation strategy introduced here opens a relatively non-destructive avenue connecting infrared nanophotonics, reconfigurable flat metasurfaces and van der Waals crystals.