Anthocyanins are responsible for grape color, an important quality factor for market acceptance. The relative proportion of cyanidin-based (cyanidin and peonidin) and delphinidin-based (delphinidin, malvidin and petunidin) anthocyanins largely determines the color variation among red/purple/blue colored grape varieties. Anthocyanin biosynthesis is under complex regulation by nutrients, hormones, and environmental cues sensed by the berry. However, the physiological mechanisms underlying these regulations are poorly understood. We developed a dynamic model, which can simulate the developmental anthocyanin composition in various genotypes and different growing conditions (light, nitrogen, carbon and water levels), to decipher the underlying regulation mechanisms. This model describes the flux partitioning by basic chemical reaction rules with total anthocyanin as input and reaction rates as parameters. Data were gathered from various experiments, which studied the developmental changes in anthocyanin composition. The model has been calibrated for several cultivars under a given growth condition and then validated by applying the model to other conditions for the same cultivar. The model can successfully simulate all the observed modifications in anthocyanin composition throughout berry ripening, providing an alternative way of phenotyping by dissecting a complicated trait (anthocyanin content and composition) into developmentally stable traits (model parameters). This model is suitable to be applied to cross progenies in order to identify potential genetic linkages with the model parameters.