Magnetic induction (MI)-operated wireless sensor networks (WSNs), due to their similar performance in air, underwater, and underground mediums, are rapidly emerging networks that offer a wide range of applications, including mine prevention, power grid maintenance, underground pipeline monitoring, and upstream oil monitoring. MI-based wireless underground sensor networks (WUSNs), utilizing small antenna coils, offer a viable solution by providing consistent channel conditions. The cross-layer protocols address the specific challenges of WUSNs, leading to improved network performance and enhanced operational capabilities in real-world applications. This work proposes a distributed cross-layer solution, leveraging the hybrid marine predator naked mole rat algorithm (MPNMRA) for MI-operated WUSNs. The solution, called DECMN (distributed energy-throughput efficient cross-layer network using MPNMRA), is designed to optimize the MI communication channels, MI relay coils (MI waveguide), and MI waveguide with 3D coils to fulfill quality of service (QoS) parameters, while achieving energy savings and throughput gains. DECMN utilizes the interactions between various layers to develop cross-layer protocols based on MPNMRA. Simulation results demonstrate the effectiveness of DECMN, offering energy savings, increased throughput, and reliable transmissions within the performance limits.