The development of emerging technologies, such as quantum computing and semiconductor electronics, emphasizes the growing significance of thermal management at cryogenic temperatures. Herein, by designing isotope interfaces based on the Golomb ruler, we achieved effective suppression of the phonon thermal transport of cryogenic graphene. The pronounced disordering of the Golomb ruler sequence results in the stronger suppression of thermal transport compared to other sequences with the same isotope doping ratio. We demonstrated that the Golomb ruler-based isotope interfaces have strong scattering and confinement effects on phonon transport via extensive molecular dynamics simulations combined with wave packet analysis, with a proper correction for the missing quantum statistics. This work provides a new stream for the design of thermal transport suppression under cryogenic conditions and is expected to expand to other fields.