Ultra-small Co3O4-C nanoparticles were synthesized with an average core size of 8.2 nm by annealing CoC nanoparticles in air at a relative low temperature. The formation mechanism of these nanoparticles can be attributed to the presence of defective C shells, the high chemical activity of ultra-small Co nanoparticles, and the gradual oxidation of the C shell during the low-temperature annealing process. The Co3O4-C nanoparticles demonstrated remarkable thermal stability at temperatures of up to 360 °C in air. Moreover, he Co3O4-C nanoparticles exhibited excellent microwave absorption performances, with an optimal reflection loss of −64.2 dB and an effective bandwidth of 6.08 GHz at a single thickness of 2.2 mm. These impressive microwave absorption properties can be attributed to the small size effects, the core-shell nanostructure, and the presence of defective C shells in the nanoparticles. Overall, the as-synthesized Co3O4-C nanoparticles show great potential for future applications as microwave absorbers, thanks to their large bandwidth, strong microwave absorption, and high thermal stability in air.