Skyrmions are topologically protected vortex-like excitations that hold promise for applications such as information processing and electron manipulation. Here we combine theoretical analysis and numerical simulations to show that skyrmions can spontaneously emerge in chiral active matter without external confinements or regulation. Strikingly, these activity-driven skyrmions can either self-organize into a periodic, stable square lattice consisting of half Néel skyrmions and antiskyrmions, where the in-plane flows display an antiferromagnetic vortex array, or undergo phase separation between skyrmions with different topological numbers. We identify that the emerging skyrmion dynamics stems from the competition between the chiral and polar coherence length scales dictated by the interplay of intrinsic chirality, polarity, and elasticity in the system. Our results reveal unanticipated topological excitations, self-organization, and phase separation in non-equilibrium systems and also suggest a potential way towards engineering complicated bespoke skyrmionic structures through manipulating active matter.