Plant and crop simulation models are powerful tools for predicting the impact of climate change, innovative crop management practices, and new trait- or gene-based breeding technologies on the production of crops and agricultural systems. In this special issue, we gather a collection of review, opinion, and primary research papers that represent the current status and future of crop and plant simulation models. The models presented in these papers have been informed and improved by new hypotheses and concepts from (eco)physiology, fueled by phenomics data, and used to bridge the gap between genes/genotypes and phenotypes.