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A highly efficient palladium-catalyzed direct C–H functionalization/annulation of BODIPYs with alkynes has been developed for the first time to construct a series of unsymmetrical benzo[b]-fused BODIPYs from readily available starting materials. These unsymmetrical benzo[b]-fused BODIPYs exhibit remarkably red-shifted emissions and larger Stokes shifts than classical BODIPY dyes. Cell imaging experiments and cytotoxicity assays demonstrate that BODIPYs 4cand 4dhave specific lysosome-labeling capacities, turn-on fluorescence emissions in cells, and low cytotoxicity.