Agrophotovoltaic (APV) system is an integrated system producing crops as well as solar energy. Because crop production underneath Photovoltaic (PV) modules requires delicate management of crops, smart farming equipment such as real-time remote monitoring sensors (e.g., thermometers, irradiance sensors, and soil moisture sensors) is installed in the APV system. This study aims at introducing a simulation-based decision support system (DSS) for smart farming in an APV system. The proposed DSS is devised to provide a mobile application service, satellite image processing, real-time data monitoring, and simulation-based performance estimation. Particularly, an agent-based simulation (ABS) is used to mimic functions of an APV system so that a data-driven function and digital twin environment are implemented in the proposed system. The ABS model is validated with field data collected from an actual APV system at the Jeollanamdo Agricultural Research and Extension Services in South Korea. As a result, farmers and engineers enable to efficiently produce solar energy without causing harmful impact on regular crop production underneath PV modules. In addition, the proposed system will contribute to enhancement of the digital twin technology in the field of agriculture.