Ensuring end-to-end cross-layer communication security in military networks by selecting covert schemes between nodes is a key solution for military communication security. With the development of communication technology, covert communication has expanded from the physical layer to the network and application layers, utilizing methods such as artificial noise, private networks, and semantic coding to transmit secret messages. However, as adversaries continuously eavesdrop on specific communication channels, the accumulation of sufficient data may reveal underlying patterns that influence concealment, and establishing a cross-layer covert communication mechanism emerges as an effective strategy to mitigate these regulatory challenges. In this article, we first survey the communication security solution based on covert communication, specifically targeting three typical scenarios: device-to-device, private network communication, and public network communication, and analyze their application scopes. Furthermore, we propose an end-to-end cross-layer covert communication scheme driven by Generative Artificial Intelligence (GenAI), highlighting challenges and their solutions. Additionally, a case study is conducted using diffusion reinforcement learning to sovle cloud edge internet of things cross-layer secure communication.