Predicting crop yield by integrating molecular basis for crop improvement attracts increasing interest but remains a great challenge due to complex biological and physiological processes across various scales. Crop physiological models have been developed and successfully used in predicting crop growth, development, and grain yield formation in response to various environments for more than half century. The crop model realized a chain of non-linear processes from canopy development, canopy photosynthesis, biomass growth and allocation, grain yield formation, and nitrogen, water, and energy balance based on detailed physiological and agronomic experiments. On the other hand, leaf biochemical photosynthesis was also modelled with relatively simple equations four decades ago, which receives wide attention due to underlying explicit biochemical mechanisms. Apart from that, the model is based on photosynthetic events occurring on leaf cellular chloroplast, which more closely represents the fundamental molecular regulation. Molecular regulatory network of photosynthesis is made clear, but such achievement in improving grain yield has not been translated well in that the molecular basis is not directly reflected in whole plant performance and lacking predicting ability from cellular level to whole plant level. Consequently, connecting both types of models will greatly accelerate the efforts of realizing the prediction of molecular outcomes in grain yield formation. Here we reviewed development of leaf and canopy photosynthesis models, and discussed the connection of both types of models to support crop improvement.