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The neutral fluorescent probes 1a-1c based on D-π-A-π-D structure, with benzopyranoquinoline as the fluorophore and the electron-donating groups at both ends, were developed, which emitted dual-channel fluorescence in different pH environments. Among them, probe 1a with both N,N -diethyl group and morpholine ring as electron-donating groups exhibited the best fluorescence performance, showing a red shift of 85 nm in dual emission at 505 nm and 590 nm, and a Stokes shift of 95 nm in both channels. The neutral 1a displayed green fluorescence specifically targeting mitochondria, while the protonated form 1a+H + resulting in red fluorescence localized in lysosomes. The ability to distinguish healthy and pathological cells such as cancer or inflammation could be achieved by observing the differences in red fluorescence within lysosomes. Probe 1a could migrate and retarget between mitochondria and lysosomes, and it was discovered by the physiological effects of chloral hydrate experiments. In addition, the dynamic changes in morphology and movement of mitochondria and lysosomes during cellular autophagy through the variation of fluorescence intensity in green and red channels induced by rapamycin and starvation conditions had been investigated deeply. [Display omitted] • Novel pH sensitive probes 1a-1c based on D-π-A-π-D structure with ICT mechanism are introduced. • Probe 1a enables distinction between healthy and pathological cells through lysosomal pH monitoring. • The dual-channel strategy of probe 1a allows independent targeting of mitochondria and lysosomes, with organelle migration capability. • Probe 1a enables long-term observation of coordinated interactions between mitochondria and lysosomes during cellular autophagy. [ABSTRACT FROM AUTHOR]