Originally discovered in prokaryotes as an adaptive immune mechanism, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems have since evolved into a highly versatile tool for precise and efficient genome editing, revolutionizing various fields of biotechnology. This review outlines the major conceptual and technological progress in CRISPR-based gene modification, highlighting its transformation from a site-specific DNA-cleaving tool into a comprehensive molecular toolbox capable of precise base conversion, programmable gene regulation, large-fragment integration, and high-throughput genome manipulation. Rather than exhaustively listing individual tools, this review emphasizes the underlying design principles, optimization strategies, and mechanistic innovations that have driven the diversification of CRISPR technologies. The authors also discuss their broad applications across medicine, agriculture, and synthetic biology, as well as current obstacles involving delivery efficiency, off-target activity, and editing fidelity. Looking ahead, continued interdisciplinary innovation will be critical to fully unlock the therapeutic and biotechnological capacity of CRISPR-based systems.