Improving photosynthesis throughout the full canopy rather than photosynthesis of only the top leaves of the canopy is central to improving crop yields. Many canopy photosynthesis models have been developed from physiological and ecological perspectives, however most do not consider heterogeneities of microclimatic factors inside a canopy, canopy dynamics and associated energetics, or competition among different plants, and most models lack a direct linkage to molecular processes. Here we described the rationale, elements, and approaches necessary to build a dynamic systems model of canopy photosynthesis. A systems model should integrate metabolic processes including photosynthesis, respiration, nitrogen metabolism, resource remobilization and photosynthate partitioning with canopy level light, CO2, water vapor distributions and heat exchange processes. In so doing a systems-based canopy photosynthesis model will enable studies of molecular ecology and dramatically improve our insight into engineering crops for improved canopy photosynthetic CO2 uptake, resource use efficiencies and yields.