Interpretations of major climatic and biological events in Earth history are, in large part, derived from the stable carbon isotope records of carbonate rocks and sedimentary organic matter(1,2). Neoproterozoic carbonate records contain unusual and large negative isotopic anomalies within long periods (10-100 million years) characterized by delta C-13 in carbonate (delta C-13(carb)) enriched to more than 15 per mil. Classically, delta C-13(carb) is interpreted as a metric of the relative fraction of carbon buried as organic matter in marine sediments(2-4), which can be linked to oxygen accumulation through the stoichiometry of primary production(3,5). If a change in the isotopic composition of marine dissolved inorganic carbon is responsible for these excursions, it is expected that records of delta C-13(carb) and delta C-13 in organic carbon (delta C-13(org)) will covary, offset by the fractionation imparted by primary production(5). The documentation of several Neoproterozoic delta C-13(carb) excursions that are decoupled from delta C-13(org), however, indicates that other mechanisms(6-8) may account for these excursions. Here we present delta C-13 data from Mongolia, northwest Canada and Namibia that capture multiple large-amplitude (over 10 per mil) negative carbon isotope anomalies, and use these data in a new quantitative mixing model to examine the behaviour of the Neoproterozoic carbon cycle. We find that carbonate and organic carbon isotope data from Mongolia and Canada are tightly coupled through multiple delta C-13(carb) excursions, quantitatively ruling out previously suggested alternative explanations, such as diagenesis(7,8) or the presence and terminal oxidation of a large marine dissolved organic carbon reservoir(6). Our data from Namibia, which do not record isotopic covariance, can be explained by simple mixing with a detrital flux of organic matter. We thus interpret delta C-13(carb) anomalies as recording a primary perturbation to the surface carbon cycle. This interpretation requires the revisiting of models linking drastic isotope excursions to deep ocean oxygenation and the opening of environments capable of supporting animals(9-11).