Enterovirus A71 (EV-A71), a member of the genus Enterovirus of the Picornaviridae family, is a major etiological agent of hand, foot, and mouth disease (HFMD) that primarily affects children <5 years of age. While subgenotype C4 has been endemic in mainland China since 1998, surveillance data indicate that the Asia-Pacific region is experiencing persistent fluctuation of subgenotype B5 strains, which demonstrates increasing epidemic potential, delineating the evolutionary landscape of EV-A71 isolates obtained from HFMD cases in the Qingdao metropolitan area during 2023-2024. From 2,083 clinical specimens, we identified 27 EV-A71-positive samples, with successful viral isolation from 19 specimens. Whole-genome phylogenetic analysis revealed the co-circulation of one endemic C4 subgenotype and two phylogenetically distinct B5 clusters. The C4 strains (26.3%, 5/19) formed a monophyletic clade with 96.95% nucleotide identity with their closest relative (Chinese strain MT708805.1, 2019), featuring conserved VP1 proteins but accumulating nonsynonymous substitutions in nonstructural regions (P2: H25Y/A177T; P3: P3L/K98R/A101T/S328N/R545K). The B5 strains (73.7%, 14/19), while retaining conserved VP1 S17 residues, diverged into two lineages on the whole-genome phylogenetic tree: The predominant B5 strains (73.7%, 14/19), while maintaining conserved VP1 S17 residues, segregated into two distinct lineages: Lineage I (n=12) contained ten strains phylogenetically clustered with Vietnam outbreak variants (2023), accompanied by two inter-type recombinant strains containing Coxsackievirus A4-derived sequences in the nonstructural P2 region and P2-P3 junction domains. Lineage II (n=2) demonstrated novel recombination patterns incorporating Coxsackievirus A2 sequences within the nonstructural P3 region. This investigation provides the first laboratory-confirmed evidence of established EV-A71 B5 subgenotype in Qingdao since surveillance initiation in 2007. Concurrent transmission of multiple EV-A71 lineages with distinct evolutionary pathways highlights the importance of implementing real-time genomic surveillance to optimize regional HFMD mitigation strategies and vaccine formulations.