Different from traditional secure communication that focuses on symbolic protection at the physical layer, semantic secure communication requires further attention to semantic-level task performance at the application layer. There is a research gap on how to comprehensively evaluate and optimize the security performance of semantic communication. In order to fill this gap, a unified semantic security metric, the cross-layer semantic secure rate (CLSSR), is defined to estimate cross-layer security requirements at both the physical layer and the application layer. Then, we formulate the maximization problem of the CLSSR with the mixed integer nonlinear programming (MINLP). We propose a hierarchical AI-native semantic secure communication network with a reinforcement learning (RL)-based semantic resource allocation scheme, aiming to ensure the cross-layer semantic security (CL-SS). Finally, we prove the convergence of our proposed intelligent resource allocation, and the simulation results demonstrate that our proposed CLSS method outperforms the traditional physical layer semantic security (PL-SS) method in terms of both task reliability and CLSSR.