Functional structural plant models of tree crops are useful tools that were introduced more than two decades ago. They can represent the growth and development of a plant through the in silico simulation of the 3D architecture in connection with physiological processes. In tree crops, physiological processes such as photosynthesis, carbon allocation, and growth are usually integrated into these models although other functions such as water and nutrient uptake are often disregarded. The implementation of the 3D architecture involves different techniques such as L-system frameworks, pipe model concepts, and Markovian models to simulate branching processes, bud fates, and elongation of stems based on the production of metamers. The simulation of root architecture is still a challenge for researchers due to a limited amount of information and experimental issues in dealing with roots because root development is not based on the production of metamers. This review aims to focus on functional-structural models of fruit tree crops, highlighting their physiological components. The potential and limits of these tools are reviewed to point out the topics that still need more attention.