Influenza B virus (IBV) has circulated in the human population for a long time, yet the evolutionary mechanisms responsible for host adaptation remain poorly understood. Here we show that recent IBV strains exhibit an enhanced ability to evade the innate immune response and an increased replication efficiency compared with earlier strains. Our data indicate that the nonstructural protein 1 (NS1) of recent IBV strains interacts with TUFM and LC3B to induce mitophagy, leading to degradation of MAVS, suppression of interferon production and enhanced viral replication. In contrast, NS1 of earlier strains displays minimal ability to trigger mitophagy-mediated MAVS degradation. Sequence analyses show that, over the past two decades, IBV has acquired a phenylalanine (F)-to-leucine (L) substitution at residue 247 of NS1, altering its interaction with LC3B. A rescued recent IBV strain carrying the NS1-L247F mutation exhibits diminished NS1-LC3B binding, impaired mitophagy, and attenuated replication. Our study shows that adaptive evolution involving a single mutation in NS1 enables mitophagy-mediated innate immune evasion, contributing to IBV adaptation to the host.