In this study, an integrated system of harvesting, collecting, and transporting willow biomass crop to a storage site was modeled and evaluated using the IBSAL simulation model. A scenario analysis was used to quantify the impacts of five major input parameters on the performance of the integrated system. These parameters include parcel size, field shape, willow yield, distance to the storage site, and type of the collection equipment. Multiple performance indicators were identified to quantify the impacts on the system such as size of the equipment fleet, effective material and field capacity of the harvester, operating costs, and waiting times. The input data were collected from 36 commercial, short-rotation, shrub willow fields in northern New York State. The simulation results indicated that crop yield and type of collection equipment have the highest impact on operating costs and the equipment fleet size. As the size of equipment fleet increases in the system, variability in the system performance tends to increase. Field shape has the least impact on the overall system performance compared to the other four input parameters. The simulation results suggest that a combination of performance indicators need to be considered to evaluate the overall performance of the dynamic and complex system of harvesting, collection and transportation in commercial willow fields. The developed IBSAL model and scenario analysis approach can assist in planning this system based on the characteristics of field, crop, and logistical equipment to reach a high system performance.