Peas are among the most popular leguminous plants, consumed by both humans and animals in large quantities. Pesticides are widely used globally to increase pea yield, and as a result, pesticide residues can be taken up by pea plants and bioaccumulate in their fruits, including peas and pods. However, there is a lack of modeling approaches available to predict residue concentrations in peas. To address this issue, a pod fruit model (specifically designed for neutral organic compounds) was proposed to simulate the bioaccumulation process of pesticide residues in pea plants, which was developed by modifying a peel-like uptake model. The simulation results, based on green pea as the modeling demonstration, reveal that moderately-lipophilic pesticides (i.e., log KOW around 3) have higher simulated concentrations in peas at harvest compared to hydrophilic (i.e., log KOW less than 0) or highly-lipophilic (i.e., log KOW over 5) pesticides, which is due to the enhanced uptake process of moderately-lipophilic compounds in the pod-pea system, such as their ability to penetrate the pod cuticle and be transported via phloem sap. The sensitivity test and variability analysis conducted in this study revealed that the degradation kinetics, including metabolism, hydrolysis, and photolysis, had a significant impact on moderately-lipophilic pesticides due to their high simulated concentrations in the pea plant. This can result in substantial loss of residue mass via degradation. The validation of the model demonstrated that the simulation results, specifically residue concentrations in the fruit, were consistent with the harvested data. However, some inconsistency was observed immediately after pesticide application, which could be attributed to plant growth dynamics and initial surface mass distributions. The proposed pod fruit model provides new insights into the bioaccumulation process of pesticide residues in pea plants and enables high-throughput simulations of residue concentrations at harvest. To enhance the performance of the pod fruit model, future research should consider plant growth dynamics, plant uptake of ionizable compounds, and initial mass distribution functions.