The precise regulation of pH in biological systems, including intracellular organelles and tissues, is essential to the normal functions of vital movement. Accurate pH determination will contribute to a better understanding of related physiological processes and the effective monitoring of physiologic derangements. Luminescence imaging and sensing are useful tools for biological study. However, the conventional intensity-based detection method suffers from low signal-to-noise ratio. Herein, we report a water-soluble ratiometric phosphorescent probe (P-pH) for measuring pH fluctuations in biological samples based on ratiometric photoluminescence imaging and photoluminescence lifetime imaging. P-pH consists of a pH-responsive iridium(III) complex, pH-inert iridium(III) complex, and hydrophilic poly(N-vinyl-2-pyrrolidone). Owing to its dual emission, P-pH was successfully used to monitor the pH variation in mitochondria and lysosomes based on the ratiometric readout. Using P-pH, the reliable evaluation of three types of pH modifiers in the zebrafish digestive tract was also realized with a distinguishable long emission lifetime. This is the first example of assessing pH modifiers in real animal models using a luminescent approach.