The invention discloses a porous carbon loaded double-crystalline phase cobalt-based fischer-tropsch symthesis catalyst and preparation method and application thereof. The catalyst takes cobalt as an active component, porous carbon as a carrier and FCC and HCP crystalline phase cobalt as active phases, the mass content of the cobalt is 29.0%-30.8%, and the mass ratio of the HCP crystalline phase to FCC crystalline phase of the cobalt is 0.42-0.97:1. During preparation, a cobalt-contained metal organic skeleton is taken as a sacrificial template which is pyrolyzed under inert atmosphere, porous carbon loaded cobalt carbide intermediates by adopting carbonization of carbon monoxide, and a catalyst precursor is obtained by gas passivation treatment; the catalyst is obtained after the precursor is subjected to hydrogenation activation treatment. The cobalt metal active phases include the FCC and HCP crystalline phases which is high in activity and good in C5+selectivity when used in fischer-tropsch synthesis reaction, high C5+space time yield is specifically achieved, and C5+products are mainly composed of gasoline and diesel compositions.