This survey delves into cross-layer energy-efficient solutions and cutting-edge security measures for Internet of Things (IoT) networks. The conventional security techniques are considered inadequate, leading to the suggestion of AI-powered intrusion detection systems and novel strategies such as blockchain integration. This research aims to promote the development of smart cities by enhancing sustainability, security, and efficiency in the industrial and agricultural sectors through the use of IoT, blockchain, AI, and new communication technologies like 5G. In this paper, we provide a comprehensive review and analysis of secure and energy-efficient cross-layer IoT frameworks based on survey of more than 100 published research articles. We highlight the significance of developing IoT security for robust and sustainable connected systems. We discuss multi-layered security approaches and ways to enhance the energy efficiency of resource-constrained devices in IoT networks. Finally, we identify open research issues and future research directions in the emerging field of cross-layer design for secure and energy-efficient IoT networks. In order to improve cybersecurity and efficiency in smart cities, the research also focuses on developing a secure, energy-efficient IoT framework integrating blockchain, artificial intelligence, and quantum-safe cryptography.