The constraint-based rMeCBM-KU50 model of cassava storage root growth was analyzed to evaluate its sensitivity, with respect to reaction flux distribution and storage root growth rate, to changes in model inputted data and constraints, including sucrose uptake rate-related data—photosynthetic rate, total leaf area, total photosynthetic rate, storage root dry weight, and biomass function-related data. These mainly varied within ±90% of the model default values, although exceptions were made for the carbohydrate (−90% to 8%) and starch (−90% to 9%) contents. The results indicated that the predicted storage root growth rate was highly affected by specific sucrose uptake rates through the total photosynthetic rate and storage root dry weight variations; whereas the carbon flux distribution, direction and partitioning inclusive, was more sensitive to the variation in biomass content, particularly the carbohydrate content. This study showed that the specific sucrose uptake rate based on the total photosynthetic rate, storage root dry weight, and carbohydrate content were critical to the constraint-based metabolic modeling and deepened our understanding of the input−output relationship—specifically regarding the rMeCBM-KU50 model—providing a valuable platform for the modeling of plant metabolic systems, especially long-growing crops.