Agrivoltaics offer a sustainable solution to the growing competition between food and energy production. However, their adoption is often constrained by the design and operation challenges associated with optimising the complex trade-off between crop yield and photovoltaic (PV) output. Digital twins can mitigate these risks, yet most agricultural digital twins operate as fragmented digital shadows, lacking high-fidelity modelling, advanced simulation, and bidirectional control capabilities. This study presents a comprehensive, end-to-end digital twin framework to address these limitations. The framework integrates a high-resolution 3D orchard model, reconstructed via UAV photogrammetry, with a CesiumJS-based web interface linked to a modular IoT architecture built on Node-RED, Message Queuing Telemetry Transport (MQTT) protocol and InfluxDB for real-time monitoring and control. A PV simulation engine supports the design, simulation and optimisation of agrivoltaic systems. Bidirectional communication was validated through remote actuation of a physical solar tracker, demonstrating integration among the 3D environment, sensor data and control systems to achieve a closed-loop digital twin. Simulation analyses suggested that panel orientation and row spacing exert a dominant influence on crop-level light distribution. Simulation results demonstrated that a 90° azimuth configuration achieved the highest daily energy yield of 53.97 kWh but reduced peak crop-level irradiance to 205 W/m². In contrast, the baseline 0° configuration offered a balanced output of 40.86 kWh with a peak light availability of 338 W/m². The validated, interoperable digital twin architecture provides a reference model for the design, simulation, monitoring and control of an agrivoltaic system, reducing investment uncertainty and supporting sustainable food–energy co-production.