This article proposes an innovative integrated framework and research methodology for data-driven simulation in transportation management through cross-sectoral collaboration. The presented study is based on a real case of synergy in the transportation of products in two sectors - agriculture and forestry. The purpose of this study is to simulate the synergistic improvement of the planning and organization of transportation of agricultural and forest products by small businesses. The benefit for participants in both economic sectors is to ensure a more efficient use of their transport and labor resources by using the opportunities of intersectoral cooperation and emergent data driven-modeling and simulation technologies. The data-driven models such as symbolic regression are used to identify patterns in data and translate the underlying relationships into the modeling formalisms needed to build computer simulation models. The proposed study was tested in real-life conditions.