Many indeterminately growing crops can show strong fluctuations in the pattern of fruit set and harvest. Our research aims at studying the different growth behaviors in pepper cultivars with the functional-structural model GreenLab. A greenhouse experiment with six pepper cultivars characterized with different fruit weight and fruit set was conducted. Detailed destructive measurements were conducted on the dimensions and fresh biomass of above-ground plant organs for each phytomer throughout the season. Parameter values were estimated through the GreenLab model using a generalized least square method for the entire growth period for all cultivars. The results indicate that the sink strength of vegetative organs in sweet pepper was higher than that of hot pepper. Wave-like patterns of source-sink ratio fluctuated more in sweet pepper compared with hot pepper. Two groups of model parameters were correlated: sink strength of leaf blade (Pb), petiole (Pp) , intemode (Ps) and the ground projection area of the leaf surface (Sp); expansion parameters of leaf blade (ab) and intemode(ae). Three-dimensional representations of individual plants were output and the architectural difference can be easily recognized. The analysis indicated that the GreenLab model had the ability to catch the growth performance of each pepper cultivar. The present results can be used for further analysis, such as linking changes of fruit and vegetative growth to fruit set, to find a plant type with better fruit distribution over time and space.