The effect of global climate cycles driven by Earth’s orbital variations on evolution is poorly understood because of difficulties achieving sufficiently-resolved records of past evolution. The fossil remains of coccolithophores, a key calcifying phytoplankton group, enable an exceptional assessment of the impact of cyclic orbital-scale climate change on evolution because of their abundance in marine sediments, and because coccolithophores demonstrate extreme morphological plasticity in response to the changing environment1,2. Recently, evolutionary genetic analyses linked broad changes in Pleistocene fossil coccolith morphology to species radiation events3. Here, using high-resolution coccolith data, we show that during the last 2.8 million years coccolithophore evolution was forced by Earth’s orbital eccentricity with rhythms of ~100,000 years and 405,000 years - a distinct spectral signature to that of coeval global climate cycles4. Simulations with an Earth System Model5 including the marine carbon cycle6 demonstrate that eccentricity directly impacts the diversity of ecological niches occurring over the annual cycle in the tropical ocean. Reduced seasonality favours species with mid-size coccoliths that bloom year-round, increasing coccolith carbonate export and burial. We posit that eccentricity pacing of phytoplankton evolution contributed to the strong 405,000-year pacing seen in records of the global carbon cycle.