Compared with classical process-based models, the functional-structural plant models provide more efficient tools to explore the impact of changes in plant structures on plant functioning. In this paper we investigated the effects of branches on the source-sink interaction for the cotton plant (Gossypium hirsutum L.) based on a two-treatment experiment conducted on cotton grown in the field: the single-stem plants and the plants with only two vegetative branches. It was observed that the branched cotton had more organs for the whole plant but the organs on the trunk were smaller than those on the single-stem cotton. The phytomer production of the branches was four or five growth cycles delayed compared with the main stem. The organs on the trunk had similar dynamics of expansion for both treatments. Effects of branches were evaluated by using the functional-structural model GREENLAB. It allowed estimating the coefficients of sink strength to differentiate the biomass acquisition abilities of organs between different physiological ages. We found that the presence of the two vegetative branches increased the ground projection area of plant leaves and had led to slight changes on the directly measured parameters; the potential relative sink strengths of organs were found similar for the two treatments.