Lithium-ion batteries (LIBs) are pivotal in modern energy storage systems, yet their safety and longevity are critically threatened by several abuses. The over-discharge is overlooked in extreme operational conditions. Over-discharge in LIBs poses significant threats to performance and safety, inducing irreversible structural and electrochemical degradation. Key mechanisms include solid electrolyte interphase (SEI) layer breakdown, copper dissolution, and dendrite-induced internal short circuits, which accelerate capacity fade and thermal runaway risks. This review systematically analyzes these degradation pathways and evaluates mitigation strategies, such as voltage cutoff circuits, advanced battery management systems (BMS), and innovative protection strategies at the material level, like prelithiation and artificial SEI layers. The work also identifies gaps in current research, advocating for improved predictive models and industrial-scale solutions to address over-discharge challenges in next-generation energy storage systems.