In Gauss-Bonnet braneworld cosmology, the Friedmann equation of our four-dimensional Universe on 3-brane is modified in a high energy regime (Gauss-Bonnet regime), while the standard expansion law is reproduced in low energies (standard regime). We investigate the Gauss-Bonnet braneworld cosmological effect on the thermal relic density of cold dark matter when the freeze-out of the dark matter occurs in the Gauss-Bonnet regime. We find that the resultant relic density is considerably reduced when the transition temperature, which connects the Gauss-Bonnet regime with the standard regime, is low enough. This result is in sharp contrast with the result previously obtained in the Randall-Sundrum braneworld cosmology, where the relic density is enhanced.