The autophagic-lysosomal pathway of microglia plays a key role in myelin debris removal in white matter damage. As the lipid-rich myelin debris are engulfed by microglia, the cellular autophagic level increases, accompanied by lysosomal dysfunction. However, several issues such as how to regulate this pathway to ensure the effective degradation of myelin debris, and maintain the balance of lipid metabolism are still to be elucidated. Recently, we have demonstrated that the excessive activation of macroautophagy/autophagy leads to lipid overload in lysosomes and lipid droplets accumulation, which could be the initiator of microglial dysfunction and secondary inflammatory white matter damage. Interestingly, staged suppression of autophagic activation in the acute phase of demyelination could benefit microglia allowing them to regain the lipid metabolism balance, and reduce the excessive accumulation of lipids, thus promoting the removal of myelin debris. The neuroprotective effects of microglial autophagy regulation may be related to intracellular linoleic acid (LA) production and PPARG pathway activation.