The invention discloses an H-3-silicon carbide PN-type isotope battery and a manufacturing method thereof. The isotope battery structurally comprises an N-type ohmic contact electrode, an N-type high-doping SiC substrate, an N-type SiC epitaxial layer and a P-type SiC epitaxial layer from bottom to top, wherein a P-type SiC ohmic contact doping layer is arranged in a part of areas at the upper part of the P-type SiC epitaxial layer; a P-type ohmic contact electrode is arranged at the top of the P-type SiC ohmic contact doping layer; an SiO2 passivation layer is arranged in an area except a P-type ohmic contact doping zone at the upper part of the P-type SiC epitaxial layer; and an H-3 radioactive isotope source is arranged above an SiO2 passivation layer. The isotope battery is novel and reasonable in design, the problem of radiation generated carrier recombination loss on the surface of H-3 can be effectively solved, and the output power and the energy conversion efficiency of the isotope battery can be effectively improved.