Nitric oxide (NO), a ubiquitous gaseous transmitter in living systems, is closely associated with physiopathological processes in the endoplasmic reticulum and lysosomes. This free radical gas is very widely but very heterogeneously distributed in the biological microenvironment, which poses a great challenge to specifically detect its localized levels in certain subcellular regions. In this study, we proposed six subcellular targeting probes by rational molecular engineering and selected two probes with optimal performance for the precise spatiotemporal identification of endoplasmic reticulum (ER) and lysosomal NO fluctuations. The probes could rapidly undergo a N-nitrosation reaction with NO at a riveted subcellular location, blocking the initial photoinduced electron transfer (PET) process and generating bright fluorescence for precise mapping of NO in the ER and lysosomes. The screened probes have ultra-sensitive reactivity and ultra-low detection limits for NO, realizing the precise depiction of exogenous and endogenous NO in the corresponding subcellular area. Fluctuations in the subcellular levels of NO during inflammation were also successfully mapped by the probes. Our work will contribute to the accurate study of the physiological and pathological consequences of subcellular NO in various biological events.