Breeding for improved leaf photosynthesis is considered as a viable approach to increase crop yield. Whether it should be improved in combination with other traits has not been assessed critically. Based on the quantitative crop model GECROS that interconnects various traits to crop productivity, we review natural variation in relevant traits, from biochemical aspects of leaf photosynthesis to morpho-physiological crop characteristics. While large phenotypic variations (sometimes >2-fold) for leaf photosynthesis and its underlying biochemical parameters were reported, few quantitative trait loci (QTL) were identified, accounting for a small percentage of phenotypic variation. More QTL were reported for sink size (that feeds back on photosynthesis) or morpho-physiological traits (that affect canopy productivity and duration), together explaining a much greater percentage of their phenotypic variation. Traits for both photosynthetic rate and sustaining it during grain filling were strongly related to nitrogen-related traits. Much of the molecular basis of known photosynthesis QTL thus resides in genes controlling photosynthesis indirectly. Simulation using GECROS demonstrated the overwhelming importance of electron transport parameters, compared with the maximum Rubisco activity that largely determines the commonly studied light-saturated photosynthetic rate. Exploiting photosynthetic natural variation might significantly improve crop yield if nitrogen uptake, sink capacity, and other morpho-physiological traits are co-selected synergistically.