Abstract: With the accelerating transition of the global energy structure toward clean and low-carbon systems and the continuous advancement of carbon peaking and carbon neutrality targets, lithium-ion batteries (LIBs) are becoming increasingly constrained by inherent limitations related to resource availability, operational safety, and overall costs. In particular, the uneven geographical distribution and limited reserves of critical strategic metals, such as lithium and cobalt, coupled with the flammability and rising costs of organic electrolyte systems, significantly hinder the long-term and large-scale deployment of LIBs in electrochemical energy storage applications. Aqueous zinc-ion batteries (AZIBs) have emerged as one of the most promising alternative energy storage technologies because of their intrinsic safety, environmental friendliness, low cost, and natural abundance of zinc resources. Despite these advantages, the practical application and commercialization of AZIBs are still severely restricted by several critical scientific and technical challenges that are predominantly associated with zinc anodes. These challenges include uncontrolled zinc dendrite growth, parasitic interfacial side reactions, and non-uniform ion transport behavior. The strong coupling of these issues leads to a rapid capacity decay, poor rate capability, and potential safety hazards, thereby significantly limiting the electrochemical performance and cycling stability of AZIB systems. These fundamental challenges are closely related to the structural characteristics and interfacial regulation capabilities of separators. As a key component connecting the cathode and anode, the separator not only serves as an ion-conducting medium but also acts as a physical barrier to prevent short circuits. Therefore, the rational design and functional modification of separators have been widely recognized as one of the most effective strategies for stabilizing zinc anodes and enhancing the overall performance of AZIBs. This review systematically summarizes recent advances in composite separators for AZIBs, with a particular focus on structural engineering and interfacial regulation strategies. First, the fundamental roles of separators in AZIB systems are clarified, emphasizing their dual functions as efficient ion transport channels and robust physical barriers. The key performance requirements and design principles of high-performance separators are then comprehensively discussed. Subsequently, the intrinsic limitations of conventional separators are analyzed, and the desirable characteristics of next-generation separators are proposed, including high ionic conductivity, superior mechanical strength, effective interfacial regulation, and multifunctional integration. Furthermore, the current research progress is categorized into four representative types of composite separators: polymer-based composite separators, biomass-derived composite separators, metal-organic framework (MOF)/covalent organic framework (COF)-based composite separators, and multifunctional integrated composite separators. For each category, the fabrication strategies, structure–property relationships, underlying mechanisms, and corresponding improvements in electrochemical performance are systematically reviewed. Special attention is paid to their roles in constructing directional ion transport pathways, enhancing Zn²⁺ transference numbers, improving mechanical resistance against dendrite penetration, and suppressing hydrogen evolution reactions and by-product formation. Finally, from the perspectives of material stability, manufacturing process scalability, cost-effectiveness, and environmental sustainability, the current challenges hindering the practical application of composite separators are critically analyzed. Future research directions are proposed, including multi-scale structural and interfacial designs, development of scalable and continuous fabrication technologies, exploration of low-cost and eco-friendly material systems, and advancement of recyclable separator technologies. This review aims to provide a comprehensive theoretical framework and practical guidance for the rational design and engineering applications of high-performance composite separators, thereby promoting the transition of aqueous zinc-ion battery technology from fundamental research to large-scale practical deployment.