Stroke is an acute cerebrovascular disease caused by cerebrovascular occlusion or hemorrhage, and approximately 84% of clinical stroke patients is suffered from cerebral ischemia (Ischemic stroke). Studies indicated that autophagy is extensively involved and prominently affects the pathophysiological development of stroke. Autophagy is a metabolic process by which delivers old proteins, damaged organelles and superfluous cytoplasmic components to lysosomes for degradation. It comprises a series of processes including activation of autophagy, formation and maturation of autophagosomes, fusion of autophagosomes with lysosomes, and digestion and degradation of autophagic substrates in autolysosomes. Autophagic flux is usually defined as autophagic/lysosomal signaling machinery. Recent studies reveal that dysfunction of autophagic flux is a critical pathogenesis of neuronal injury after ischemic stroke. However, disruption in any step in the autophagic/lysosomal pathway can lead to impairment of autophagic flux. This article is to be reviewed from the following four items. Firstly, excessive activation of autophagy, deficiency of autophagosome formation, fusion blockage of autophagosomes with lysosomes, as well as lysosomal inefficiency can drive dysfunction of autophagic flux and thereby aggravating neuronal injury. Secondly, fusion disruption between autophagosomes and lysosomes is an important cause of autophagic/lysosomal dysfunction in neurons. Consequently, a massive of autophagic substrates is accumulated within cells to worsen post-stroke damage. Thirdly, the fusion of autophagosomes with lysosomes is mainly mediated by the membrane-to-membrane fusion machinery via the three core elements: NSF (N-ethyl-maleimide sensitive factor ATPase), SNAP (soluble NSF attachment protein), and SNAREs (soluble NSF attachment protein receptors). SNAP is an adaptor attaching NSF to SNAREs, which are the proteins directly mediate the membrane fusion. After membrane-membrane fusion, SNAREs must be reactivated by NSF for the next round of fusion. It is vital that NSF is the sole ATPase to regenerate active SNAREs. SNF inactivation represses the reactivation of SNAREs and thereby disrupting the fusion between autophagosomes and lysosomes after ischemic stroke. Subsequently, the autophagic/lysosomal dysfunction in neurons is created to aggravate the neurological injury. Additionally, the insufficiency of the tethering proteins and inefficiency of the GTPases are also the pathologies to interrupt the fusion between autophagosomes and lysosomes. Accordingly, the impaired autophagic flux in neurons may be restored by facilitating fusion of autophagosomes with lysosomes, via pharmacological intervene, gene modulation, microenvironment amelioration, or mTOR signaling regulation. Finally, based on the mechanism of autolysosome formation, more therapeutic clues may be sought to alleviate neurological injury after ischemic stroke.