Second-order continuous phase transitions are characterized by symmetry breaking with order parameters. Topological orders of electrons, characterized by the topological index defined in momentum space, provide a distinct perspective for phase transitions, which are categorized as quantum phase transitions not being accompanied by symmetry breaking. However, there are still limited observations of counterparts in real space. Here we show a real-space topological phase transition in a chiral magnet MnGe, hosting a periodic array of hedgehog and antihedgehog topological spin singularities. This transition is driven by the pair annihilation of the hedgehogs and antihedgehogs acting as monopoles and antimonopoles of the emergent electromagnetic field. Observed anomalies in the magnetoresistivity and phonon softening are consistent with the theoretical prediction of critical phenomena associated with enhanced fluctuations of emergent field near the transition. This finding reveals a vital role of topology of the spins in strongly correlated systems.