Precise in vivo tracking of hydrogen peroxide is still challenging due to its dynamic complexity and intrinsic background interference. Herein, we describe a rational design strategy to construct asymmetric aza-boron-dipyrromethane derivative (BODIPY)-based ratiometric probes for in vivo tracking H(2)O(2), which are composed of a near-infrared aza-BODIPY core, active targeting group, and H(2)O(2)-specific recognition unit. We take advantage of two terminal functionalized conjunctions in the bis-condensed aza-BODIPY by rationally introducing carbonyl group as an electron-deficiency linker for regulating intramolecular charge transfer-induced wavelength shift and by attaching hydrophilic polyethylene glycol-biotin segment as the active targeting moiety. The probe BP(5)-NB-OB features several striking characteristics: (i) ratiometric near infrared response in both absorption and emission spectra; (ii) active targeting ability (biotin receptor-mediated endocytosis) with excellent biocompatibility; and (iii) in vivo tracking of endogenous H(2)O(2). It was demonstrated that the probe BP(5)-NB-OB was successfully utilized for tracking endogenous H(2)O(2) in living cells and tumor-bearing mice, providing opportunities to insight into H(2)O(2) related diseases for clinical application.