Early vigour and drought tolerance are essential for rice (Oryza sativa L .) crop establishment and final yield in rainfed, vegetative drought prone environments. However, recently, a negative linkage between these complex traits was pointed out within the rice genetic diversity, making the seedling performance under drought dependent on complex, dynamic trade-offs among several elemental traits difficult to separate experimentally. This study explored the way Ecomeristem, a FSPM of rice morphogenesis and phenotypic plasticity, can support the analysis of the genetic and environmental control of traits underlying rice genetic diversity in terms of early vigour and drought tolerance. Once validated, the model was calibrated for 176 genotypes within a diversity panel studied in a drought phenotyping, greenhouse experiment. Model parameters controlling early vigour were heritable and thus relevant for genetic studies. Parameters reproduced the negative linkages pointed out experimentally among vigour and drought tolerance traits and clustered genotypes consistently according to experimental results. The need to improve model formalisms regarding C assimilation and gas exchanges is pointed out. Opportunities and limits to support the phenotyping and genetic study of complex traits and the exploration of rice ideotypes for drought prone environments are discussed.