A series of five BODIPY derivatives with triarylamine (TPA) moieties on their 3-, 5-, or 8-positions were reported, which showed wide-range fluorescence emissions across red and near infrared regions in their aggregation states. The influences of numbers and substituted positions of TPA groups on the optical and aggregation-induced emission (AIE) properties of these BODIPYs as well as organelle-specific imaging in live cells were investigated. The TPA groups installed at 3-/5-positions of BODIPY could effectively enlarge the conjugated system and red-shift the absorption and emission bands (λemmax up to 815 nm). In contrast, the TPA group linked to 8-position of BODIPY core has little contribution to decrease the HOMO-LUMO energy gap. Importantly, regardless the substitution positions of TPA groups, all these TPA-substituted BODIPYs (BTs) showed remarkable AIE performance and possessed high molar extinction absorption (up to ∼ 63000 M−1 cm−1), two-photon absorption (up to 171 GM at 870 nm), and large Stokes shifts. The BODIPY with one TPA group (BT1 and FBT1) showed lipid droplets-specific localization while BODIPY with two and three TPA groups (BT2, BT3 and FBT2) preferred to enrich in lysosomes. These BODIPYs all have been successfully used in tracking the dynamic behaviors of lipid droplets or lysosomes in living cells. Furthermore, BT1 and FBT1 can quantitatively detect the overexpression of lipid droplets, and BT3 has been successfully used to observe lysosomes behaviors of lipophagy process in living cells. This work systematically studied the influence of the number and position of TPA units on the optical properties and AIE-activities of BODIPYs, which not only enriched the BODIPY-based AIE NIR probes for organelle-specific imaging in live cells, but also provided a practical strategy for the effective construction of organic dyes with NIR AIE activity.