Tomato (Solanum lycopersicum L.) is an important vegetable crop and often cultivated in regions exposed to salinity and high temperatures (HT) which change plant architecture, decrease canopy light interception and disturb physiological functions. However, the long-term effects of salinity and HT combination (S+HT) on plant growth are still unclear. A dynamic functional-structural plant model (FSPM) of tomato was parameterized and evaluated for different levels of S+HT combinations. The evaluated model was used to quantify the contributions of morphological changes (architectural effects) and physiological disturbances (non-architectural effects) on the reduction of shoot dry mass under S+HT. The model predicted architectural variables with high accuracy (>85%), which ensured the reliability of the model analyses. HT enhanced architectural effects but reduced non-architectural effects of salinity on dry mass production. The stronger architectural effects of salinity under HT could not be counterbalanced by the smaller non-architectural effects. Therefore, long-term influences of HT on shoot dry mass under salinity were negative at the whole plant level. Our model analysis highlights the importance of plant architecture at canopy level in studying the plant responses to the environments and shows the merits of dynamic FSPMs as heuristic tools.