Sixth Generation (6G) communication networks are expected to evolve into AI-native, highly autonomous ecosystems that integrate communication, computing, sensing, and artificial intelligence. While these capabilities enable unprecedented connectivity and intelligent services, they also create a highly heterogeneous security and privacy landscape that cannot be addressed through isolated, technology-specific solutions. This paper presents a comprehensive survey of security and privacy in AI-native 6G networks from a cross-layer perspective. We first examine the fragmentation of existing security and privacy approaches across emerging technologies, network architectures, AI systems, and standardization efforts, motivating the need for a unified security and privacy framework. Building upon this framework, we develop a cross-layer threat taxonomy encompassing infrastructure, network and architectural, AI, privacy, and security management domains, and analyze representative threats across key AI-native 6G technologies. Furthermore, we map these threats to corresponding cross-layer countermeasures, including standards harmonization as a security function, and identify critical research gaps and future priorities for secure, interoperable, and trustworthy AI-native 6G ecosystems. Finally, we discuss future research directions toward realizing secure, privacy-preserving, resilient, and globally interoperable 6G networks. This survey provides researchers, practitioners, and standardization communities with a holistic foundation for the design, evaluation, and deployment of trustworthy AI-native 6G systems.

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