The integration of digital technology with agriculture is unlocking a new era of intelligent farm management. The Digital Twin (DT) framework in agriculture has evolved as a major transformation by providing a real-time, dynamic, optimised, and predictive approach between physical agroecosystems and their digital counterparts. The DTs are applied to address the challenges of modern agriculture, where in-situ monitoring, optimisation, and adaptability are critical factors for enhancing sustainability. Therefore, this study explores the design, application, and evolution of DT frameworks, which are developed and customised for agricultural system optimisation. A structured hierarchical design is proposed to integrate agricultural systems with IoT-enabled sensing, AI-driven analytics, and predictive models. This approach allows real-time monitoring, forecasting, and autonomous control across a wide range of agricultural processes. Three case studies from crucial domains like yield forecasting, autonomous machinery coordination, and predictive disease management are considered. The significance of DTs is demonstrated by analysing resource efficiency, environmental impact, and decision-making adaptability on the farm. Finally, challenges for implementing DTs in agriculture, like heterogeneous data sources, model fidelity, computational overhead, and barriers to adoption among smallholder farmers, are explored, and the mitigation strategies using advanced AI frameworks are discussed. The implementation of DTs can become core infrastructure for smart agriculture by enhancing its scalability, interoperability, and adaptability. This study evaluates a fundamental and practical outline by bridging the physical and virtual barriers to make resilient, sustainable, and optimized agricultural operations in real time.