Over the past years, significant progresses have been made in the field of nanopores, particularly in single-molecule analysis, sequencing, and diagnostic applications, certainly underscoring the versatility of stochastic nanopore sensing. The subsequent advances in functionalizing protein nanopores with tailored properties or reactive handles have greatly expanded their detection capabilities, where customized computational design shows promise in driving nanopore functionalization and applications toward unprecedented flexibility. In this review, we provide a comprehensive perspective of the various engineering strategies employed in protein nanopores and the roles of functionalized nanopore in single-molecule sensing and sequencing. Additionally, we elucidate the interplay between functionalization strategies and their intended applications, highlighting promising implementation scenarios. We believe that the ongoing advancements in functionalization technologies will promote innovations in de novo pore design and propel nanopore protein sequencing.