The rapid growth of semiconductor technology and globalization of the integrated circuit (IC) supply chain have significantly increased concerns regarding hardware security in Very Large Scale Integration (VLSI) systems. Modern electronic devices, ranging from consumer electronics to defense and healthcare applications, rely heavily on highly integrated semiconductor chips. However, the complexity of contemporary VLSI designs and the involvement of multiple third-party vendors during design and fabrication have exposed hardware systems to various security threats, including hardware Trojans, reverse engineering, intellectual property piracy, side-channel attacks, and counterfeit integrated circuits. These threats can compromise system confidentiality, integrity, and availability, leading to severe economic and security consequences. This paper presents a comprehensive study of hardware security challenges in VLSI systems and reviews recent research developments in secure chip design methodologies. Furthermore, a Secure Adaptive Hardware Protection Framework (SAHPF) is proposed to enhance resilience against emerging hardware attacks. The framework integrates logic locking, physical unclonable functions, runtime monitoring, and secure authentication mechanisms to provide multilayer security. Performance evaluation indicates that the proposed approach improves security robustness while maintaining acceptable area, power, and delay overheads. The findings demonstrate that proactive security integration during the VLSI design cycle is essential for ensuring trustworthy semiconductor systems.