Uncoordinated 51-like kinase 1 (ULK1) is a well-characterized initiator of canonical autophagy under basal or pathological conditions. Porcine haemagglutinating encephalomyelitis virus (PHEV), a neurotropic betacoronavirus (beta-CoV), impairs ULK1 kinase but hijacks autophagy to facilitate viral proliferation. However, the machinery of PHEV-induced autophagy initiation upon ULK1 kinase deficiency remains unclear. Here, the time course of PHEV infection showed a significant accumulation of autophagosomes (APs) in nerve cells in vivo and in vitro. Utilizing the ULK1-knockout neuroblastoma cells, we have identified that ULK1 was not essential for productive AP formation induced by PHEV. In vitro phosphorylation studies discovered that mTORC1-regulated ULK1 activation stalls during PHEV infection, whereas the AP biogenesis was controlled by AMPK-driven BECN1 phosphorylation. A lack of BECN1 is sufficient to block LC3 lipidation and disrupt recruitment of the LC3-ATG14 complex. Moreover, BECN1 acts as a bona fide substrate for ULK1-independent neural autophagy, and ectopic expression of BECN1 somewhat enhances PHEV replication. These findings highlight a novel machinery of non-canonical autophagy independent of ULK1 that bypasses the conserved initiation circuit of AMPK-mTORC1-ULK1, providing new insights into the interplay between neurotropic beta-CoV and the host. IMPORTANCE The ongoing COVID-19 pandemic alongside the outbreaks of SARS and MERS pose betacoronavirus (beta-CoV) as a global public health challenge. Coronaviruses subvert, haijack, or utilize autophagy to promote proliferation, thus exploring the cross-talk between beta-CoV and autophagy of great significance in confronting future beta-CoV outbreaks. Porcine haemagglutinating encephalomyelitis virus (PHEV) is a highly neurotropic beta-CoV and invades the central nervous system (CNS) in pigs, but understanding of the pathogenesis for PHEV-induced neurological dysfunction yet limited. Here, we discovered a novel regulatory principle of neural autophagy initiation during PHEV infection, where productive autophagosome (AP) biogenesis bypassing the multifaceted regulation of ULK1 kinase. The PHEV-triggered non-canonical autophagy underscores the complex interactions of virus-host, and will help in the development of therapeutic strategies targeting non-canonical autophagy to treat beta-CoV disease.