If you'd like a more general overview of climate proxies, I'd recommend reading this website.
One of the non-isotope proxies for CO2 dating back tens of millions of years is the stomatal index record. Stomata are microscopic "mouths" on plant leaves that open and close to let in CO2 but keep H2O from escaping. In a higher CO2 environment, plants grow more stomata per unit area. Stomata can be counted in some plant fossils, and this can be used as a proxy.
Most of the proxies are too complex to be modelled backwards to get the atmospheric CO2 values that caused them, so they must be calibrated against more "absolute" records such as bubbles in ice cores.