Near-infrared (NIR) fluorescent probes are increasingly popular in biological imaging and sensing, as long-wavelength (650–900 nm) excitation and emission have the advantages of minimum photodamage, deep tissue penetration, and minimum interference from autofluorescence in living systems. Here, a series of long-wavelength BODIPY dyes SPC, DC-SPC, DPC, and DC-DPC are synthesized conveniently and efficiently. They exhibit excellent photophysical properties in far red to near-infrared region, including large extinction coefficients, high fluorescence quantum yields, good photostability, and reasonable two-photon absorption cross section. Comparison of single-molecular imaging confirms that DPC is a much more efficient and more photostable NIR fluorophore than the commonly used Cy5. Also importantly, two kinds of convenient functionalization sites have been reserved: the aryl iodide for organometallic couplings and the terminal alkyne groups for click reactions. Further derivatives DC-SPC-PPh3 exhibit specificity to localize in mitochondria. The introduction of triphenylphosphonium (TPP) moieties mediates its hydrophilic–lipophilic balance and makes DC-SPC-PPh3 appropriate for cell labeling. Their long-wavelength emission at ∼650 nm can efficiently avoid the spectral crosstalk with other probes emitting in the visible light region. Superior photostability, low cytotoxicity, and two-photon excitable properties demonstrate its utility as a standard colocalizing agent to estimate the other probes’ local distribution.