In the last few years, architectural studies have been carried out on the aerial development of apple trees taking into account their genotypic diversity. At the same time root architecture remained under-investigated. This led us to develop new research regarding tree physiology in terms of interactions with both the environment and root architecture. The present work had a double objective: (i) the development of a structure function modeling approach relying on the description of the tree’s aerial structure and physiology; (ii) the investigation of the structure and growth dynamics of the root system in relation to those of the aerial part. The experiments were carried out at INRA experimental station, Melgueil (France). Two-year-old apple trees of two INRA hybrids (X3305 and X6407) and seven-year-old trees of two commercial varieties (Fuji and Braeburn) were studied. Aerial systems were described and digitized taking into account both topology and geometry of tree constituents. The growth dynamics of tree aerial parts were inferred from space-time colored labeling, while the root systems were studied by means of land rhizotrons. Two physiological functions were examined: transpiration and carbon assimilation. Photosynthesis responses to different environmental conditions (solar radiation, humidity and temperature) were analyzed at a leaf level with a Licor 6200 system. These observations were used to parameterize the RATP model (Radiation Absorption, Transpiration and Photosynthesis). Experimental data that were recorded at the branch scale were used to assess the RATP model for transpiration, sap flow being measured by means of the heat balance method. This paper presents work in progress for the first application of a structure function model to apple trees