Abstract: The rapid growth of electric vehicle and energy storage sectors has driven a substantial increase in global lithium demand, highlighting the urgent need to recover lithium from spent lithium-ion batteries as a strategy to alleviate resource scarcity, reduce costs, and mitigate environmental impacts. Conventional recovery methods, including pyrometallurgy and hydrometallurgy, are constrained by high energy consumption, significant environmental burdens, and limited selectivity, thereby hindering their feasibility for large-scale and sustainable lithium recycling. In this context, bioleaching has emerged as a promising alternative owing to its mild operating conditions, environmental compatibility, and relatively low cost; however, leaching efficiency and process stability remain suboptimal. This review focuses on strategies to enhance lithium bioleaching from spent lithium-ion batteries, beginning with an elucidation of the fundamental mechanisms through which functional microorganisms mediate lithium extraction. Based on these mechanisms, enhancement strategies are systematically discussed from both microbial and engineering perspectives, with multiscale coupled mechanisms serving as the central framework. At the microbial level, recent advances in functional strain screening—including the isolation of indigenous microorganisms and the development of non-acidophilic systems—as well as adaptive evolution and synthetic biology approaches (e.g., genetic engineering and the construction of synthetic microbial consortia), are reviewed for their capacity to improve acidolysis, complexation, and redox-mediated leaching processes. At the engineering level, the transition from conventional parameter optimization (e.g., pH, carbon source, and pulp density) to data- and model-driven process optimization is examined, alongside the contribution of process scheduling to enhancing leaching kinetics and operational stability. Furthermore, synergistic strategies that combine bioleaching with physical, chemical, or electrochemical interventions are critically analyzed. To address key bottlenecks in bioleaching-based lithium recovery, including metabolic supply limitations, microbe–material interfacial processes, material evolution, selective dissolution, and mass-transfer constraints, future research should prioritize the following directions: (1) integrated multi-omics analyses combined with network modeling to elucidate metabolic allocation, stress-response regulation, and microbe–material interfacial dynamics under complex environmental conditions; synthetic biology tools can enable rational design of microbial strains and consortia to enhance efficiency and selectivity; (2) mechanistic studies of lithium handling, encompassing lithium sensing, transmembrane transport, and intracellular accumulation, which can facilitate the identification or design of engineerable, lithium-specific functional modules, enabling engineered microorganisms to achieve in situ selective lithium recovery during dissolution; and (3) from an engineering perspective, a shift from single-factor empirical optimization to cross-scale, multi-level, and intelligent process control strategies, maximizing system-wide efficiency. The integration of life-cycle assessment and techno-economic analysis is also recommended to systematically evaluate environmental performance and economic feasibility, thereby providing a robust foundation for stable scale-up and industrial application. In summary, this review systematically examines the mechanisms and enhancement strategies of lithium bioleaching from spent lithium-ion batteries and aims to promote the synergistic advancement of microbial innovation and engineering integration, ultimately providing theoretical and technical guidance for establishing a sustainable, efficient, and industrially viable framework for green lithium recovery.