Unveiling the nature of the pseudogap and its relation to both superconductivity and antiferromagnetic Mott insulators, the pairing mechanism, and a non-Fermi liquid phase is a key issue for understanding high temperature superconductivity in cuprates.We here show that antiparallel magnetic order can be reasonably and naturally predicted in hole-doped CuO2 planes by starting from the ground state of a weakly doped antiferromagnetic insulator, where a Skyrmion-type three-dimensional spin texture is created around the doped hole. The superconducting transition temperature Tc can be understood in terms of the temperature at which long-range antiparallel magnetic ordering is established, resulting in the magnetically mediated superconducting state with phase-coherent Cooper pairs. Upon heating above Tc, long-range phase coherence in the pair state is lost, but the pair condensate still survives on the medium-range length scale, transforming to the pseudogap state with charge and magnetic orders. We believe the present model provides a key initial point to unravel a wide variety of the apparently complex phenomena related to high temperature cuprate superconductors.