In this study, a highly selective chemosensor ML based on a BODIPY fluorescent chromophore was synthesized for sequential recognition of Cu²⁺ and HSO₃⁻ in a CH₃OH/H₂O (99 : 1 v/v) system, which contained three recognition sites and its structure characterized by ¹H NMR, ¹³C NMR and ESI-HR-MS. The sensor ML showed an obvious “on–off” fluorescence quenching response toward Cu²⁺ and the ML-Cu²⁺ complex showed an “off–on” fluorescence enhancement response toward HSO₃⁻. The detection limit of the sensor ML was 0.36 μM to Cu²⁺ and 1.4 μM to HSO₃⁻. In addition, the sensor ML showed a 1 : 3 binding stoichiometry to Cu²⁺ and the recovery rate of ML-Cu²⁺ complex identifying HSO₃⁻ could be over 70%. Sensor ML showed remarkable detection ability in a pH range of 4–8.