Neurodegenerative diseases (NDs) are a wide variety of disorders characterized by the progressive and irreversible loss of neuronal structure and functions leading to cognitive impairments. The common types of NDs include Alzheimer’s disease, amyotrophic lateral sclerosis, Huntington’s disease, and Parkinson’s disease. The sharing pathological hallmarks of these diseases are the aberrant aggregation and amyloid deposition. However, the underlying molecular mechanisms of protein misfolding and aberrant aggregation remain elusive. Amyloid protein is prone to aggregate from its native disordered monomeric state into well-ordered amyloid fibril state via nucleation-dependent polymerization mechanism, in which follows sigmoidal growth kinetics with three steps: lag phase, growth phase, and plateau phase. The formation and subsequent distribution of these pathological amyloid fibrils are closely related to the onset and progression of NDs. Additionally, the aberrant aggregation of these disease-associated proteins proceeds via liquid-liquid phase separation (LLPS) and liquid-to-solid phase transition (LSPT) leading to amyloid fibril formation in the condensed phase. The phase transition from liquid-like droplets or dynamic condensates to solid-like hydrogel or amyloids is intimately linked to the pathogenesis of several NDs. In this Review, we discuss two typical pathways of amyloid fibrils formation. One route involves aggregation in the bulk solution environment, proceeding via nucleation and elongation steps to form amyloid fibrils. In this scenario, protein aggregation initiates with the nucleation step to form oligomeric nuclei. Then the nuclei serve as templates for the subsequent elongation step ultimately leading to the formation of amyloid fibrils. When sufficient fibrils have formed during self-assembly, the secondary nucleation is triggered to generate new species of oligomers and fibrillar aggregates. The other route of fibril formation occurs in the condensed phase through LLPS and LSPT to form amyloid aggregates and deposits. The occurrence of a phase separation leads to the liquid-like droplets formation during the early stage of aggregation. Over time, these dynamic biomolecular condensates gradually solidify and ultimately evolve into a hydrogel state enriched by amyloid aggregates through a phase transition process. Evidence indicates that pathological phase transitions are early events in the pathogenesis of several NDs. It should be noted that these two routes are not independent or mutually exclusive. They are interconnected and function cooperatively during aberrant aggregation. The pathological progression of NDs is closely related to the dominant aggregation pathway involved in aberrant aggregation. Moreover, the molecular mechanisms underlying the formation of pathogenic amyloid deposits are intricately linked to the structural and functional characteristics of aggregates. These aggregates may not only directly participate in fibrillization, but also indirectly promote the development of NDs by affecting the normal physiological cellular functions. Therefore, in-depth research on the structural and functional properties of both intermediates and fibrils is of great significance for understanding the molecular mechanisms of protein misfolding and aberrant aggregation. Overall, this paper reviews the amyloid deposition and pathological phase transitions in NDs. By delving into the molecular mechanisms of amyloid fibrillization, the aim is to better understand the pathogenesis of NDs, and to provide valuable insights into the development of therapeutic strategies targeting amyloid aggregation and aberrant phase transition.